rs3132131

Variant names:

• chr6-32931708-A-G
• rs3132131

Your query was ambiguous. Multiple possible variants found:

• chr6-32931708-A-G
• chr6-32931708-A-T

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 0.731 in 152,186 control chromosomes in the GnomAD database, including 41,778 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 0.73 (41778 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.881
• Publications: 30 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 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: 0.731 AC: 111162 AN: 152066 Hom.: 41720 Cov.: 33

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.731 AC: 111273 AN: 152186 Hom.: 41778 Cov.: 33 AF XY: 0.722 AC XY: 53717 AN XY: 74368

African (AFR) AF: 0.918 AC: 38132 AN: 41558

American (AMR) AF: 0.676 AC: 10335 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2318 AN: 3472

East Asian (EAS) AF: 0.659 AC: 3407 AN: 5172

South Asian (SAS) AF: 0.703 AC: 3390 AN: 4820

European-Finnish (FIN) AF: 0.579 AC: 6122 AN: 10568

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

European-Non Finnish (NFE) AF: 0.664 AC: 45134 AN: 67988

Other (OTH) AF: 0.748 AC: 1578 AN: 2110

Alfa AF: 0.694 Hom.: 108282

Bravo AF: 0.748

Asia WGS AF: 0.666 AC: 2319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.85
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs3132131; hg19: chr6-32899485;