6-31675622-T-C

Variant names:

• chr6-31675622-T-C
• rs3115667

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 0.746 in 152,168 control chromosomes in the GnomAD database, including 42,665 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 0.75 (42665 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 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: 0.746 AC: 113394 AN: 152050 Hom.: 42633 Cov.: 33

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.746 AC: 113473 AN: 152168 Hom.: 42665 Cov.: 33 AF XY: 0.752 AC XY: 55960 AN XY: 74386

African (AFR) AF: 0.673 AC: 27932 AN: 41484

American (AMR) AF: 0.771 AC: 11789 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.884 AC: 3066 AN: 3470

East Asian (EAS) AF: 0.973 AC: 5040 AN: 5178

South Asian (SAS) AF: 0.839 AC: 4049 AN: 4826

European-Finnish (FIN) AF: 0.815 AC: 8636 AN: 10596

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50322 AN: 68006

Other (OTH) AF: 0.764 AC: 1614 AN: 2112

Alfa AF: 0.751 Hom.: 118521

Bravo AF: 0.740

Asia WGS AF: 0.905 AC: 3147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.015
DANN	Benign	0.15
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs3115667; hg19: chr6-31643399;