rs3132562

Variant names:

• chr6-31081215-G-A
• rs3132562

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 0.648 in 147,172 control chromosomes in the GnomAD database, including 31,080 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 (31080 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.648 AC: 95342 AN: 147080 Hom.: 31058 Cov.: 25

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.648 AC: 95396 AN: 147172 Hom.: 31080 Cov.: 25 AF XY: 0.646 AC XY: 46142 AN XY: 71390

African (AFR) AF: 0.707 AC: 28227 AN: 39932

American (AMR) AF: 0.595 AC: 8753 AN: 14720

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2905 AN: 3466

East Asian (EAS) AF: 0.646 AC: 3230 AN: 4998

South Asian (SAS) AF: 0.715 AC: 3403 AN: 4758

European-Finnish (FIN) AF: 0.603 AC: 5370 AN: 8910

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41212 AN: 67132

Other (OTH) AF: 0.680 AC: 1403 AN: 2062

Alfa AF: 0.632 Hom.: 16029

Bravo AF: 0.648

Asia WGS AF: 0.679 AC: 2363 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.62
DANN	Benign	0.40
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs3132562; hg19: chr6-31048992;