rs3132291

Variant names:

• chr9-134441072-G-A
• rs3132291

Your query was ambiguous. Multiple possible variants found:

• chr9-134441072-G-A
• chr9-134441072-G-C
• chr9-134441072-G-T

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 0.611 in 152,036 control chromosomes in the GnomAD database, including 30,905 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 0.61 (30905 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.744 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: 0.612 AC: 92974 AN: 151916 Hom.: 30916 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.611 AC: 92968 AN: 152036 Hom.: 30905 Cov.: 32 AF XY: 0.612 AC XY: 45456 AN XY: 74312

African (AFR) AF: 0.335 AC: 13894 AN: 41444

American (AMR) AF: 0.634 AC: 9691 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2571 AN: 3470

East Asian (EAS) AF: 0.648 AC: 3338 AN: 5148

South Asian (SAS) AF: 0.520 AC: 2498 AN: 4808

European-Finnish (FIN) AF: 0.735 AC: 7780 AN: 10588

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 50967 AN: 67968

Other (OTH) AF: 0.631 AC: 1333 AN: 2112

Alfa AF: 0.686 Hom.: 53307

Bravo AF: 0.597

Asia WGS AF: 0.572 AC: 1991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.49
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs3132291; hg19: chr9-137332918; COSMIC: COSV62683926;