rs3812163

Variant names:

• chr6-7725527-A-T
• rs3812163

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.385 in 151,886 control chromosomes in the GnomAD database, including 11,826 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.39 (11826 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 48 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58498 AN: 151768 Hom.: 11825 Cov.: 31

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.365

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.385 AC: 58525 AN: 151886 Hom.: 11826 Cov.: 31 AF XY: 0.381 AC XY: 28315 AN XY: 74236

African (AFR) AF: 0.281 AC: 11658 AN: 41434

American (AMR) AF: 0.304 AC: 4648 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1381 AN: 3468

East Asian (EAS) AF: 0.238 AC: 1228 AN: 5152

South Asian (SAS) AF: 0.529 AC: 2536 AN: 4792

European-Finnish (FIN) AF: 0.440 AC: 4633 AN: 10536

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31034 AN: 67920

Other (OTH) AF: 0.360 AC: 759 AN: 2108

Alfa AF: 0.424 Hom.: 1695

Bravo AF: 0.366

Asia WGS AF: 0.344 AC: 1198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.63
PhyloP100		0.039

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3812163; hg19: chr6-7725760;