rs3757167

Variant names:

• chr6-136819855-T-C
• rs3757167

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 0.532 in 151,996 control chromosomes in the GnomAD database, including 21,820 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 0.53 (21820 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.607 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: 0.532 AC: 80802 AN: 151876 Hom.: 21811 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.532 AC: 80837 AN: 151996 Hom.: 21820 Cov.: 32 AF XY: 0.532 AC XY: 39483 AN XY: 74282

African (AFR) AF: 0.420 AC: 17409 AN: 41444

American (AMR) AF: 0.618 AC: 9433 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2021 AN: 3472

East Asian (EAS) AF: 0.496 AC: 2567 AN: 5174

South Asian (SAS) AF: 0.546 AC: 2633 AN: 4818

European-Finnish (FIN) AF: 0.535 AC: 5636 AN: 10538

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39433 AN: 67970

Other (OTH) AF: 0.535 AC: 1127 AN: 2106

Alfa AF: 0.557 Hom.: 4145

Bravo AF: 0.532

Asia WGS AF: 0.525 AC: 1826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	16
DANN	Benign	0.86
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs3757167; hg19: chr6-137140993; COSMIC: COSV59248424;