rs9262648

Variant names:

• chr6-31061396-C-A
• rs9262648

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 0.223 in 152,074 control chromosomes in the GnomAD database, including 3,859 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 0.22 (3859 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.245 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: 0.223 AC: 33902 AN: 151956 Hom.: 3861 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.223 AC: 33904 AN: 152074 Hom.: 3859 Cov.: 32 AF XY: 0.224 AC XY: 16658 AN XY: 74334

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.236

Alfa AF: 0.232 Hom.: 2406

Bravo AF: 0.219

Asia WGS AF: 0.175 AC: 611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9262648; hg19: chr6-31029173;