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SNV:1-54625879-C-T (GRCh38)

Dataset

gnomAD v4.1.0

	Exomes	Genomes	Total
Filters	No data	Pass	Not in exomes
Allele Count	-	41738	41738
Allele Number	-	146558	146558
Allele Frequency	-	0.2848	0.2848
Grpmax Filtering AF (95% confidence)	-	0.3316 East Asian	0.3531 Middle Eastern
Number of homozygotes	-	6509	6509

External Resources

Feedback

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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


	384	894	77	0.4295
	1474	3444	318	0.4280
	116	280	25	0.4143
	3506	9388	635	0.3735
	1683	4874	281	0.3453
	22389	67058	3745	0.3339
	645	2014	97	0.3203
	4510	14558	693	0.3098
	1343	4660	207	0.2882
	5688	39388	431	0.1444
XX	21281	75428	3274	0.2821
XY	20457	71130	3235	0.2876
Total	41738	146558	6509	0.2848

Include:ExomesGenomes


	130	272	33	0.4779
	114	262	23	0.4351
	120	324	18	0.3704
	138	398	23	0.3467
	17	94	3	0.1809
	16	170	1	0.09412
	2	26	0	0.07692
XX	197	538	35	0.3662
XY	340	1008	66	0.3373
Total	537	1546	101	0.3473

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


	378	1010	64	0.3743
	333	980	50	0.3398
	188	668	27	0.2814
	265	976	47	0.2715
	130	1262	8	0.1030
XX	654	2444	93	0.2676
XY	640	2452	103	0.2610
Total	1294	4896	196	0.2643


	Overall	5588	38326	0.1458
European	2351	7378	0.3187
African	3237	30948	0.1046
Total	5588	38326	0.1458

Related Variants

Liftover

The following GRCh37 variant lifts over to this variant:

1-55091552-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 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. ACOT11
  1. ENST00000371316.3
    HGVSc
    c.1630-4855C>T
2. 1. ENST00000416119.1
    Ensembl canonical transcript for
    HGVSc
    n.281+2279G>A

In Silico Predictors

CADD: 2.73
SpliceAI: 0.00
Pangolin: 0.00
phyloP: 0.778

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: 2.733e+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	2.733e+7
inbreeding_coeff	0.042
AS_FS	1.11
AS_MQ	59.689
AS_MQRankSum	-0.04
AS_pab_max	1
AS_QUALapprox	2.733e+7
AS_QD	16.254
AS_ReadPosRankSum	0.109
AS_SOR	0.728
AS_VarDP	6.2257
AS_VQSLOD	2.058

Read Data

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