rs3130542

Variant names:

• chr6-31264334-A-G
• rs3130542

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 0.807 in 151,944 control chromosomes in the GnomAD database, including 49,579 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 0.81 (49579 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 73 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.827 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: 0.807 AC: 122596 AN: 151826 Hom.: 49545 Cov.: 31

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.807 AC: 122680 AN: 151944 Hom.: 49579 Cov.: 31 AF XY: 0.806 AC XY: 59887 AN XY: 74262

African (AFR) AF: 0.834 AC: 34587 AN: 41468

American (AMR) AF: 0.797 AC: 12161 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3172 AN: 3470

East Asian (EAS) AF: 0.823 AC: 4186 AN: 5088

South Asian (SAS) AF: 0.761 AC: 3622 AN: 4760

European-Finnish (FIN) AF: 0.793 AC: 8374 AN: 10564

Middle Eastern (MID) AF: 0.815 AC: 238 AN: 292

European-Non Finnish (NFE) AF: 0.792 AC: 53849 AN: 68024

Other (OTH) AF: 0.828 AC: 1745 AN: 2108

Alfa AF: 0.804 Hom.: 125054

Bravo AF: 0.809

Asia WGS AF: 0.779 AC: 2711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	8.1
DANN	Benign	0.85
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3130542; hg19: chr6-31232111;