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SNV:1-54581999-C-G (GRCh38)

Dataset

gnomAD v4.1.0

	Exomes	Genomes	Total
Filters	No data	Pass	Not in exomes
Allele Count	-	633	633
Allele Number	-	152238	152238
Allele Frequency	-	0.004158	0.004158
Grpmax Filtering AF (95% confidence)	-	0.09922 East Asian	0.09922 East Asian
Number of homozygotes	-	36	36

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


	551	5170	36	0.1066
	23	4824	0	0.004768
	10	2104	0	0.004753
	9	3472	0	0.002592
	17	15304	0	0.001111
	15	68018	0	0.0002205
	8	41534	0	0.0001926
	0	10606	0	0.000
	0	294	0	0.000
	0	912	0	0.000
XX	274	77806	19	0.003522
XY	359	74432	17	0.004823
Total	633	152238	36	0.004158

Include:ExomesGenomes


	30	440	2	0.06818
	1	302	0	0.003311
	1	362	0	0.002762
	0	198	0	0.000
	0	280	0	0.000
	0	100	0	0.000
	0	28	0	0.000
XX	13	588	1	0.02211
XY	19	1122	1	0.01693
Total	32	1710	2	0.01871


	124	990	6	0.1253
	2	990	0	0.002020
	0	1286	0	0.000
	0	680	0	0.000
	0	1022	0	0.000
XX	70	2476	4	0.02827
XY	56	2492	2	0.02247
Total	126	4968	6	0.02536


	Overall	17	15214	0.001117
Amerindigenous	15	4371	0.003432
European	2	9393	0.0002129
African	0	1450	0.000
Total	17	15214	0.001117

Related Variants

Liftover

The following GRCh37 variant lifts over to this variant:

1-53521883-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 0 transcripts in 0 genes.

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

In Silico Predictors

CADD: 1.24
phyloP: -1.59

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: 1-53056000-53057000

Expected	Observed	Constraint
196.6	168	Z = 2.04 o/e = 0.85

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: 6.501e+5 (genome samples)

Site quality approximation for all variants with 0.002 <= AF < 0.005.

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

Metric	Genome samples
SiteQuality	6.501e+5
inbreeding_coeff	0.109
AS_FS	0
AS_MQ	59.942
AS_MQRankSum	0
AS_pab_max	1
AS_QUALapprox	6.501e+5
AS_QD	14.711
AS_ReadPosRankSum	0.386
AS_SOR	0.703
AS_VarDP	4.6454
AS_VQSLOD	6.719

Read Data

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