rs9267947

chr6-32243441-A-Gchr6-32243441-A-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 0.635 in 121,020 control chromosomes in the GnomAD database, including 23,321 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 0.64 (23321 hom., cov: 16)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 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: 0.635 AC: 76800 AN: 120936 Hom.: 23277 Cov.: 16

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.597

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.635 AC: 76883 AN: 121020 Hom.: 23321 Cov.: 16 AF XY: 0.639 AC XY: 36816 AN XY: 57652

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.646

Alfa AF: 0.460 Hom.: 12056

Bravo AF: 0.574

Asia WGS AF: 0.621 AC: 2135 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9267947; hg19: chr6-32211218; COSMIC: COSV50756306;