rs9262656

Positions:

• chr6-31066487-A-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 0.223 in 152,050 control chromosomes in the GnomAD database, including 3,853 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 (3853 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694

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 (AMR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33890 AN: 151936 Hom.: 3855 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.223 AC: 33891 AN: 152050 Hom.: 3853 Cov.: 32 AF XY: 0.224 AC XY: 16657 AN XY: 74304

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: 0.293

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.237

Alfa AF: 0.233 Hom.: 2293

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	-0.99
CADD	Benign	0.21
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9262656; hg19: chr6-31034264;