rs3130542

chr6-31264334-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.828

Alfa AF: 0.801 Hom.: 53646

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130542; hg19: chr6-31232111;