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SNV:4-1816707-G-A (GRCh38)

Dataset

gnomAD v4.1.0

	Exomes	Genomes	Total
Filters	Pass	Pass
Allele Count	349	48	397
Allele Number	1455590	152236	1607826
Allele Frequency	0.0002398	0.0003153	0.0002469
Grpmax Filtering AF (95% confidence)	0.004559 East Asian	0.004014 East Asian	0.004645 East Asian
Number of homozygotes	0	0	0

External Resources

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Genetic Ancestry Group Frequencies

gnomAD
HGDP
1KG
Local Ancestry


	232	44672	0.005193
	102	29504	0.003457
	25	90878	0.0002751
	16	62256	0.0002570
	1	6052	0.0001652
	1	59814	0.00001672
	19	1175086	0.00001617
	1	74916	0.00001335
	0	63736	0.000
	0	912	0.000
XX	212	810324	0.0002616
XY	185	797502	0.0002320
Total	397	1607826	0.0002469

Include:ExomesGenomes


	3	440	0.006818
	0	198	0.000
	0	302	0.000
	0	280	0.000
	0	100	0.000
	0	362	0.000
	0	28	0.000
XX	2	588	0.003401
XY	1	1122	0.0008913
Total	3	1710	0.001754


	7	990	0.007071
	0	1286	0.000
	0	680	0.000
	0	1022	0.000
	0	990	0.000
XX	4	2476	0.001616
XY	3	2492	0.001204
Total	7	4968	0.001409

Related Variants

Liftover

The following GRCh37 variant lifts over to this variant:

4-1818434-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 1 transcript 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. LETM1
  1. ENST00000302787.3
    MANE Select transcript for LETM1
    HGVSc
    c.1931+20C>T

In Silico Predictors

CADD: 0.410
SpliceAI: 0.00
Pangolin: 0.00
phyloP: -3.49

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.

ClinVar

ClinVar Variation ID: 1900773
Conditions: not provided
Germline classification: Benign
Review status: criteria provided, single submitter (1 star)
Last evaluated: September 13, 2023

or find more information on the ClinVar website. Data displayed here is from ClinVar's February 1, 2025 release.

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: 3.305e+5 (exome samples), 4.349e+4 (genome samples)

Site quality approximation for all variants with 0.0002 <= AF < 0.0005.

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

Metric	Exome samples	Genome samples
SiteQuality	3.305e+5	4.349e+4
inbreeding_coeff	0.005	-3.217e-4
AS_FS	4.822e-16	0.522
AS_MQ	59.996	60
AS_MQRankSum	0	0.352
AS_pab_max	1	1
AS_QUALapprox	3.304e+5	4.349e+4
AS_QD	13.292	12.877
AS_ReadPosRankSum	0.127	0.337
AS_SOR	0.703	0.636
AS_VarDP	4.3955	3.5285
AS_VQSLOD	8.867	5.972

Read Data

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