rs9262651

Variant names:

• chr6-31061678-C-T
• rs9262651

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 0.232 in 152,056 control chromosomes in the GnomAD database, including 4,151 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 0.23 (4151 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.25 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: 0.232 AC: 35218 AN: 151938 Hom.: 4153 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.232 AC: 35221 AN: 152056 Hom.: 4151 Cov.: 32 AF XY: 0.233 AC XY: 17282 AN XY: 74326

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.240

Alfa AF: 0.245 Hom.: 2567

Bravo AF: 0.227

Asia WGS AF: 0.181 AC: 631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9262651; hg19: chr6-31029455;