rs9271640

Positions:

• chr6-32624423-T-C
• chr6-32624423-T-G

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 0.762 in 151,652 control chromosomes in the GnomAD database, including 44,449 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 0.76 (44449 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 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: 0.762 AC: 115509 AN: 151536 Hom.: 44422 Cov.: 30

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.762 AC: 115594 AN: 151652 Hom.: 44449 Cov.: 30 AF XY: 0.758 AC XY: 56160 AN XY: 74086

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.808

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.803

Alfa AF: 0.781 Hom.: 13362

Bravo AF: 0.765

Asia WGS AF: 0.649 AC: 2262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	8.9
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9271640; hg19: chr6-32592200; COSMIC: COSV70073303;