6-31240563-C-T

Variant names:

• chr6-31240563-C-T
• rs3095250

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 0.576 in 151,890 control chromosomes in the GnomAD database, including 25,422 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 0.58 (25422 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87511 AN: 151772 Hom.: 25408 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.576 AC: 87564 AN: 151890 Hom.: 25422 Cov.: 31 AF XY: 0.570 AC XY: 42346 AN XY: 74260

African (AFR) AF: 0.604 AC: 25008 AN: 41400

American (AMR) AF: 0.547 AC: 8361 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2399 AN: 3472

East Asian (EAS) AF: 0.559 AC: 2883 AN: 5158

South Asian (SAS) AF: 0.444 AC: 2137 AN: 4816

European-Finnish (FIN) AF: 0.482 AC: 5077 AN: 10526

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39818 AN: 67936

Other (OTH) AF: 0.563 AC: 1183 AN: 2100

Alfa AF: 0.587 Hom.: 81788

Bravo AF: 0.581

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.56
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs3095250; hg19: chr6-31208340;