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SNV:1-53629280-C-T (GRCh38)

Dataset

gnomAD v4.1.0

	Exomes	Genomes	Total
Filters	Pass	Pass
Allele Count	8	140967	140975
Allele Number	8 *	152288	152296 *
Allele Frequency	1.000	0.9257	0.9257
Grpmax Filtering AF (95% confidence)	0.3416 European (non-Finnish)	0.9533 European (non-Finnish)	0.9534 European (non-Finnish)
Number of homozygotes	4	65409	65413

Warning This variant is covered in fewer than 50% of individuals in gnomAD v4.1.0 exomes. Allele frequency estimates may not be reliable.

External Resources

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Genetic Ancestry Group Frequencies

Note Local ancestry data is available for this variant by selecting the tab below. See our blog post on local ancestry inference for Admixed American samples in gnomAD for more information.

gnomAD
HGDP
1KG
Local Ancestry


	885	912	429	0.9704
	65282	68036	31323	0.9595
	10187	10620	4888	0.9592
	1990	2112	938	0.9422
	275	294	129	0.9354
	3243	3472	1508	0.9340
	13919	15302	6347	0.9096
	37121	41556	16576	0.8933
	4227	4826	1852	0.8759
	3846	5166	1423	0.7445
XX	72302	77834	33644	0.9289
XY	68673	74462	31769	0.9223
Total	140975	152296	65413	0.9257

Include:ExomesGenomes


	28	28	14	1.000
	288	302	137	0.9536
	95	100	45	0.9500
	265	280	126	0.9464
	164	198	69	0.8283
	298	362	124	0.8232
	327	440	124	0.7432
XX	526	588	238	0.8946
XY	939	1122	401	0.8369
Total	1465	1710	639	0.8567

Warning Because of low sample sizes for HGDP populations, allele frequencies may not be representative.


	993	1022	482	0.9716
	608	680	271	0.8941
	875	990	388	0.8838
	1136	1286	501	0.8834
	711	990	254	0.7182
XX	2161	2476	953	0.8728
XY	2162	2492	943	0.8676
Total	4323	4968	1896	0.8702


	Overall	13834	15212	0.9094
European	9130	9481	0.9630
African	1125	1287	0.8741
Amerindigenous	3579	4444	0.8054
	Overall	36146	40446	0.8937
European	7308	7753	0.9426
African	28838	32693	0.8821
Total	49980	55658	0.8980

Related Variants

Other Alternate Alleles

This variant is multiallelic. Other alternate alleles are:

1-54153664-C-A

Liftover

The following GRCh37 variant lifts over to this variant:

1-54619337-C-T
View variant in gnomAD v2.1.1

Nearby Variants

View variants located within 20 bases of this variant.

Variant Effect Predictor

This variant falls on 4 transcripts in 2 genes.

Note The gene symbols shown below are provided by VEP and may differ from the symbol shown on gene pages.

5' UTR
1. CDCP2
  1. ENST00000371330.1
    HGVSc
    c.-742G>A
intron
1. 1. ENST00000637610.1
    Ensembl canonical transcript for
    HGVSc
    c.304-483G>A
  2. ENST00000311841.7
    HGVSc
    c.*179-483G>A
  3. ENST00000525949.1
    HGVSc
    n.93-8851G>A

In Silico Predictors

CADD: 3.06
SpliceAI: 0.00
Pangolin: 0.00
phyloP: 0.618

Note For more detailed and up to date SpliceAI and Pangolin predictions, please visit our SpliceAI Lookup browser

Genomic Constraint of Surrounding 1kb Region

This variant does not have non coding constraint data for the surrounding region.

Age Distribution

Exome
Genome

Variant carriers
All individuals

Include heterozygous variant carriersInclude homozygous variant carriersCompare to all individuals

Sequencing types:

Genotype Quality Metrics

Genotype quality
Depth
Allele balance for heterozygotes

Exome
Genome

Variant carriers
All individuals

Compare to all individualsSequencing types:

Site Quality Metrics

Metric distribution
All metric values

Exome
Genome

Metric: Sequencing types:

Value: 6.304e+6 (exome samples), 1.709e+8 (genome samples)

Site quality approximation for all variants with AF >= 0.5.

Note: These are site-level quality metrics, they may be unpredictable for multi-allelic sites.

Metric	Exome samples	Genome samples
SiteQuality	6.304e+6	1.709e+8
inbreeding_coeff	0.993	0.032
AS_FS	4.822e-16	1.446e-15
AS_MQ	59.999	59.997
AS_MQRankSum	0	-0.044
AS_pab_max	1	1
AS_QUALapprox	6.304e+6	1.709e+8
AS_QD	31.595	30.772
AS_ReadPosRankSum	0	0.317
AS_SOR	0.769	0.683
AS_VarDP	5.3000	6.7446
AS_VQSLOD	7.512	20.183

Read Data

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