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SNV:3-38846594-G-T (GRCh38)

Dataset

gnomAD v4.1.0

	Exomes	Genomes	Total
Filters	Pass	Pass
Allele Count	4287	901	5188
Allele Number	687862 *	152182	840044 *
Allele Frequency	0.006232	0.005921	0.006176
Grpmax Filtering AF (95% confidence)	0.006738 Middle Eastern	0.005251 European (non-Finnish)	0.006624 Middle Eastern
Number of homozygotes	30	3	33

Warning This variant is covered in fewer than 50% of individuals in gnomAD v4.1.0 exomes. Allele frequency estimates may not be reliable.

External Resources

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Genetic Ancestry Group Frequencies

gnomAD
HGDP
1KG
Local Ancestry


	975	60048	8	0.01624
	306	19508	3	0.01569
	26	2750	0	0.009455
	245	35928	2	0.006819
	2874	518440	15	0.005544
	313	58582	2	0.005343
	273	59616	3	0.004579
	175	43380	0	0.004034
	1	912	0	0.001096
	0	40880	0	0.000
XX	2429	406236	10	0.005979
XY	2759	433808	23	0.006360
Total	5188	840044	33	0.006176

Include:ExomesGenomes


	4	302	0.01325
	2	280	0.007143
	0	198	0.000
	0	440	0.000
	0	100	0.000
	0	362	0.000
	0	28	0.000
XX	3	588	0.005102
XY	3	1122	0.002674
Total	6	1710	0.003509


	8	1022	0.007828
	2	680	0.002941
	2	1286	0.001555
	1	990	0.001010
	0	990	0.000
XX	6	2476	0.002423
XY	7	2492	0.002809
Total	13	4968	0.002617


	Overall	202	40398	0.005000
African	165	32338	0.005102
European	37	8060	0.004591
	Overall	63	15210	0.004142
African	10	1590	0.006289
European	53	8812	0.006015
Amerindigenous	0	4808	0.000
Total	265	55608	0.004766

Related Variants

Other Alternate Alleles

This variant is multiallelic. Other alternate alleles are:

3-38846594-G-A

Liftover

The following GRCh37 variant lifts over to this variant:

3-38888085-G-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 1 gene.

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

3' UTR
1. SCN11A
  1. ENST00000302328.9
    MANE Select transcript for SCN11A
    HGVSc
    c.*100C>A
  2. ENST00000668754.1
    HGVSc
    c.*100C>A

In Silico Predictors

CADD: 1.40
SpliceAI: 0.00
Pangolin: 0.00
phyloP: -0.431

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: 3-38846000-38847000

Expected	Observed	Constraint
98.9	97	Z = 0.19 o/e = 0.98

ClinVar

ClinVar Variation ID: 1201052
Conditions: not provided
Germline classification: Likely benign
Review status: criteria provided, multiple submitters, no conflicts (2 stars)
Last evaluated: September 22, 2018

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: 2.959e+6 (exome samples), 7.914e+5 (genome samples)

Site quality approximation for all variants with 0.005 <= AF < 0.01.

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

Metric	Exome samples	Genome samples
SiteQuality	2.959e+6	7.914e+5
inbreeding_coeff	0.058	7.087e-4
AS_FS	0	0
AS_MQ	60	59.994
AS_MQRankSum	0	-0.065
AS_pab_max	1	1
AS_QUALapprox	2.958e+6	7.914e+5
AS_QD	14.488	13.855
AS_ReadPosRankSum	0	0.231
AS_SOR	0.692	0.698
AS_VarDP	5.3100	4.7568
AS_VQSLOD	8.852	20.791

Read Data

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