rs3761672

chr9-37908661-G-Achr9-37908661-G-T

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 0.552 in 151,950 control chromosomes in the GnomAD database, including 23,726 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 0.55 (23726 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 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: 0.552 AC: 83759 AN: 151832 Hom.: 23661 Cov.: 32

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.552 AC: 83886 AN: 151950 Hom.: 23726 Cov.: 32 AF XY: 0.553 AC XY: 41056 AN XY: 74262

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.552

Alfa AF: 0.510 Hom.: 9400

Bravo AF: 0.564

Asia WGS AF: 0.636 AC: 2213 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	5.7
Dann	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3761672; hg19: chr9-37908658; COSMIC: COSV54252535;