chr6-31238839-A-G

Variant names:

• chr6-31238839-A-G
• rs3130531

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 0.647 in 152,060 control chromosomes in the GnomAD database, including 31,783 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 0.65 (31783 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 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: 0.647 AC: 98299 AN: 151942 Hom.: 31763 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.647 AC: 98367 AN: 152060 Hom.: 31783 Cov.: 32 AF XY: 0.646 AC XY: 48042 AN XY: 74336

African (AFR) AF: 0.702 AC: 29101 AN: 41476

American (AMR) AF: 0.642 AC: 9819 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2200 AN: 3466

East Asian (EAS) AF: 0.701 AC: 3622 AN: 5168

South Asian (SAS) AF: 0.563 AC: 2707 AN: 4812

European-Finnish (FIN) AF: 0.654 AC: 6914 AN: 10570

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41835 AN: 67970

Other (OTH) AF: 0.642 AC: 1354 AN: 2108

Alfa AF: 0.634 Hom.: 64206

Bravo AF: 0.649

Asia WGS AF: 0.578 AC: 2012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.4
DANN	Benign	0.65
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs3130531; hg19: chr6-31206616;