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SNV:1-57904426-T-C (GRCh38)

Dataset

gnomAD v4.1.0

	Exomes	Genomes	Total
Filters	No data	Pass	Not in exomes
Allele Count	-	31279	31279
Allele Number	-	152102	152102
Allele Frequency	-	0.2056	0.2056
Grpmax Filtering AF (95% confidence)	-	0.2974 East Asian	0.2974 East Asian
Number of homozygotes	-	3614	3614

External Resources

Feedback

Report an issue with this variant

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


	340	910	72	0.3736
	1595	5144	237	0.3101
	12247	41432	1802	0.2956
	1290	4822	180	0.2675
	74	290	11	0.2552
	792	3472	87	0.2281
	458	2116	58	0.2164
	3177	15298	324	0.2077
	10094	68008	772	0.1484
	1212	10610	71	0.1142
XX	15805	77724	1787	0.2033
XY	15474	74378	1827	0.2080
Total	31279	152102	3614	0.2056

Include:ExomesGenomes


	80	198	18	0.4040
	30	100	4	0.3000
	123	440	21	0.2795
	74	278	13	0.2662
	64	360	5	0.1778
	45	302	6	0.1490
	2	28	0	0.07143
XX	143	586	25	0.2440
XY	275	1120	42	0.2455
Total	418	1706	67	0.2450

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


	419	1284	68	0.3263
	284	988	43	0.2874
	268	990	38	0.2707
	153	680	19	0.2250
	141	1022	14	0.1380
XX	632	2474	99	0.2555
XY	633	2490	83	0.2542
Total	1265	4964	182	0.2548


	Overall	11849	40324	0.2938
African	10623	32552	0.3263
European	1226	7772	0.1577
	Overall	3150	15208	0.2071
African	456	1294	0.3524
Amerindigenous	1010	4558	0.2216
European	1684	9356	0.1800
Total	14999	55532	0.2701

Related Variants

Liftover

The following GRCh37 variant lifts over to this variant:

1-58526416-G-A
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 2 transcripts in 2 genes.

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

intron
1. 1. ENST00000419596.1
    Ensembl canonical transcript for
    HGVSc
    n.169+437G>A
2. DAB1
  1. ENST00000485760.5
    HGVSc
    n.387+89767C>T

In Silico Predictors

CADD: 1.25
Pangolin: 0.0100
phyloP: -0.206

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

Genomic Constraint of Surrounding 1kb Region

Genomic constraint values displayed are for the region: 1-58060000-58061000

Expected	Observed	Constraint
70.4	57	Z = 1.59 o/e = 0.81

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: 4.615e+7 (genome samples)

Site quality approximation for all variants with 0.2 <= AF < 0.5.

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

Metric	Genome samples
SiteQuality	4.615e+7
inbreeding_coeff	0.034
AS_FS	2.893e-15
AS_MQ	59.997
AS_MQRankSum	-0.016
AS_pab_max	1
AS_QUALapprox	4.615e+7
AS_QD	22.635
AS_ReadPosRankSum	0.421
AS_SOR	0.687
AS_VarDP	6.3094
AS_VQSLOD	22.174

Read Data

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