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SNV:1-54834828-G-A (GRCh38)

Dataset

gnomAD v4.1.0

	Exomes	Genomes	Total
Filters	No data	Pass	Not in exomes
Allele Count	-	60347	60347
Allele Number	-	152080	152080
Allele Frequency	-	0.3968	0.3968
Grpmax Filtering AF (95% confidence)	-	0.5284 African/African American	0.5284 African/African American
Number of homozygotes	-	12754	12754

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


	22159	41476	5934	0.5343
	2737	5176	729	0.5288
	128	294	31	0.4354
	6220	15284	1278	0.4070
	839	2112	171	0.3973
	1195	3470	195	0.3444
	22749	67984	3825	0.3346
	1291	4812	196	0.2683
	242	910	31	0.2659
	2787	10562	364	0.2639
XX	31238	77752	6644	0.4018
XY	29109	74328	6110	0.3916
Total	60347	152080	12754	0.3968

Include:ExomesGenomes


	126	198	39	0.6364
	57	100	16	0.5700
	199	438	43	0.4543
	126	280	30	0.4500
	10	28	2	0.3571
	99	302	17	0.3278
	113	360	24	0.3139
XX	247	588	56	0.4201
XY	483	1118	115	0.4320
Total	730	1706	171	0.4279

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


	707	1284	197	0.5506
	516	990	140	0.5212
	300	680	66	0.4412
	361	1022	60	0.3532
	258	990	35	0.2606
XX	1088	2474	257	0.4398
XY	1054	2492	241	0.4230
Total	2142	4966	498	0.4313


	Overall	21520	40368	0.5331
African	18822	32585	0.5776
European	2698	7783	0.3467
	Overall	6166	15194	0.4058
African	651	1209	0.5385
Amerindigenous	1860	4483	0.4149
European	3655	9502	0.3847
Total	27686	55562	0.4983

Related Variants

Liftover

The following GRCh37 variant lifts over to this variant:

1-55300501-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 1 gene.

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

intron
1. LEXM
  1. ENST00000371273.4
    MANE Select transcript for LEXM
    HGVSc
    c.1185-6973G>A
  2. ENST00000358193.7
    HGVSc
    c.1185-6788G>A

In Silico Predictors

CADD: 0.805
SpliceAI: 0.00
Pangolin: 0.00
phyloP: -1.30

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: 1-54834000-54835000

Expected	Observed	Constraint
143.4	126	Z = 1.46 o/e = 0.88

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: 6.471e+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	6.471e+7
inbreeding_coeff	0.043
AS_FS	9.643e-16
AS_MQ	59.993
AS_MQRankSum	-0.02
AS_pab_max	1
AS_QUALapprox	6.471e+7
AS_QD	19.163
AS_ReadPosRankSum	0.347
AS_SOR	0.691
AS_VarDP	6.5285
AS_VQSLOD	21.882

Read Data

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