rs3130532

Variant names:

• chr6-31240676-A-G
• rs3130532

Your query was ambiguous. Multiple possible variants found:

• chr6-31240676-A-G
• chr6-31240676-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 0.882 in 152,202 control chromosomes in the GnomAD database, including 59,281 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 0.88 (59281 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 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: 0.882 AC: 134075 AN: 152084 Hom.: 59226 Cov.: 31

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.972

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.882 AC: 134185 AN: 152202 Hom.: 59281 Cov.: 31 AF XY: 0.882 AC XY: 65604 AN XY: 74398

African (AFR) AF: 0.934 AC: 38796 AN: 41530

American (AMR) AF: 0.876 AC: 13396 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.972 AC: 3376 AN: 3472

East Asian (EAS) AF: 0.840 AC: 4350 AN: 5180

South Asian (SAS) AF: 0.872 AC: 4210 AN: 4830

European-Finnish (FIN) AF: 0.851 AC: 9000 AN: 10570

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.854 AC: 58080 AN: 68010

Other (OTH) AF: 0.907 AC: 1918 AN: 2114

Alfa AF: 0.866 Hom.: 106380

Bravo AF: 0.887

Asia WGS AF: 0.876 AC: 3050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.51
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs3130532; hg19: chr6-31208453;