rs3757167

Positions:

• chr6-136819855-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.535

Alfa AF: 0.560 Hom.: 4066

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

Splicing

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

Publications

LitVar

Other links and lift over

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