6-31523223-A-G

Variant names:

• chr6-31523223-A-G
• rs3095227

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 0.792 in 152,146 control chromosomes in the GnomAD database, including 47,798 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 0.79 (47798 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 24 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 = 0.878 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120352 AN: 152028 Hom.: 47757 Cov.: 31

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.869

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.792 AC: 120446 AN: 152146 Hom.: 47798 Cov.: 31 AF XY: 0.797 AC XY: 59303 AN XY: 74370

African (AFR) AF: 0.822 AC: 34099 AN: 41494

American (AMR) AF: 0.812 AC: 12415 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2981 AN: 3470

East Asian (EAS) AF: 0.899 AC: 4664 AN: 5186

South Asian (SAS) AF: 0.862 AC: 4144 AN: 4810

European-Finnish (FIN) AF: 0.809 AC: 8570 AN: 10588

Middle Eastern (MID) AF: 0.863 AC: 252 AN: 292

European-Non Finnish (NFE) AF: 0.751 AC: 51047 AN: 67996

Other (OTH) AF: 0.789 AC: 1663 AN: 2108

Alfa AF: 0.770 Hom.: 47614

Bravo AF: 0.793

Asia WGS AF: 0.823 AC: 2865 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	1.7
DANN	Benign	0.74
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3095227; hg19: chr6-31491000;