6-31243273-A-G

Variant names:

• chr6-31243273-A-G
• rs3130695

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 0.795 in 152,008 control chromosomes in the GnomAD database, including 48,024 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 (48024 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• 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 = 0.802 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: 0.795 AC: 120730 AN: 151890 Hom.: 47987 Cov.: 31

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.795 AC: 120816 AN: 152008 Hom.: 48024 Cov.: 31 AF XY: 0.794 AC XY: 59002 AN XY: 74298

African (AFR) AF: 0.810 AC: 33527 AN: 41414

American (AMR) AF: 0.785 AC: 11998 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3152 AN: 3472

East Asian (EAS) AF: 0.765 AC: 3958 AN: 5176

South Asian (SAS) AF: 0.731 AC: 3516 AN: 4808

European-Finnish (FIN) AF: 0.808 AC: 8542 AN: 10568

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53434 AN: 67976

Other (OTH) AF: 0.801 AC: 1693 AN: 2114

Alfa AF: 0.797 Hom.: 92202

Bravo AF: 0.793

Asia WGS AF: 0.757 AC: 2634 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.32
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs3130695; hg19: chr6-31211050;