rs3957146

Variant names:

• chr6-32713753-T-C
• rs3957146

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 0.0917 in 152,304 control chromosomes in the GnomAD database, including 817 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 0.092 (817 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 42 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.175 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: 0.0917 AC: 13950 AN: 152186 Hom.: 816 Cov.: 33

Gnomad AFR AF: 0.0372

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0752

Gnomad SAS AF: 0.0687

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0918

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

GnomAD4 genome AF: 0.0917 AC: 13970 AN: 152304 Hom.: 817 Cov.: 33 AF XY: 0.0936 AC XY: 6968 AN XY: 74466

African (AFR) AF: 0.0374 AC: 1554 AN: 41574

American (AMR) AF: 0.180 AC: 2760 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 588 AN: 3472

East Asian (EAS) AF: 0.0756 AC: 392 AN: 5188

South Asian (SAS) AF: 0.0685 AC: 331 AN: 4830

European-Finnish (FIN) AF: 0.110 AC: 1163 AN: 10600

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6831 AN: 68016

Other (OTH) AF: 0.0908 AC: 192 AN: 2114

Alfa AF: 0.115 Hom.: 3158

Bravo AF: 0.0985

Asia WGS AF: 0.0600 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.1
DANN	Benign	0.44
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs3957146; hg19: chr6-32681530;