6-31265733-T-C

Variant names:

• chr6-31265733-T-C
• rs2248880

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 0.196 in 152,166 control chromosomes in the GnomAD database, including 3,258 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 0.20 (3258 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) 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: 0.196 AC: 29833 AN: 152048 Hom.: 3258 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.0519

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.196 AC: 29836 AN: 152166 Hom.: 3258 Cov.: 32 AF XY: 0.192 AC XY: 14247 AN XY: 74392

African (AFR) AF: 0.130 AC: 5387 AN: 41500

American (AMR) AF: 0.146 AC: 2227 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1245 AN: 3472

East Asian (EAS) AF: 0.0522 AC: 271 AN: 5192

South Asian (SAS) AF: 0.181 AC: 871 AN: 4816

European-Finnish (FIN) AF: 0.174 AC: 1844 AN: 10608

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17175 AN: 67972

Other (OTH) AF: 0.192 AC: 405 AN: 2112

Alfa AF: 0.227 Hom.: 1707

Bravo AF: 0.191

Asia WGS AF: 0.116 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.63
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2248880; hg19: chr6-31233510;