6-31213248-C-T

Variant names:

• chr6-31213248-C-T
• rs9263948

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.122 in 151,552 control chromosomes in the GnomAD database, including 1,241 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 0.12 (1241 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.157 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: 0.122 AC: 18505 AN: 151452 Hom.: 1239 Cov.: 30

Gnomad AFR AF: 0.0983

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.122 AC: 18525 AN: 151552 Hom.: 1241 Cov.: 30 AF XY: 0.127 AC XY: 9365 AN XY: 73990

African (AFR) AF: 0.0984 AC: 4066 AN: 41314

American (AMR) AF: 0.162 AC: 2463 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 618 AN: 3466

East Asian (EAS) AF: 0.108 AC: 555 AN: 5130

South Asian (SAS) AF: 0.140 AC: 669 AN: 4790

European-Finnish (FIN) AF: 0.187 AC: 1939 AN: 10390

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7626 AN: 67938

Other (OTH) AF: 0.171 AC: 360 AN: 2108

Alfa AF: 0.115 Hom.: 1359

Bravo AF: 0.122

Asia WGS AF: 0.133 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.58
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9263948; hg19: chr6-31181025; COSMIC: COSV55132498;