rs3130637

chr6-31520368-A-Gchr6-31520368-A-T

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 0.786 in 660,704 control chromosomes in the GnomAD database, including 205,350 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 0.79 (47761 hom., cov: 32)
  • Exomes 𝑓: 0.78 (157589 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.769

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 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: 0.791 AC: 120286 AN: 151980 Hom.: 47720 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.787

GnomAD4 exome AF: 0.784 AC: 398684 AN: 508606 Hom.: 157589 AF XY: 0.789 AC XY: 214029 AN XY: 271214

Gnomad4 AFR exome AF: 0.824

Gnomad4 AMR exome AF: 0.805

Gnomad4 ASJ exome AF: 0.855

Gnomad4 EAS exome AF: 0.901

Gnomad4 SAS exome AF: 0.869

Gnomad4 FIN exome AF: 0.795

Gnomad4 NFE exome AF: 0.749

Gnomad4 OTH exome AF: 0.775

GnomAD4 genome AF: 0.791 AC: 120380 AN: 152098 Hom.: 47761 Cov.: 32 AF XY: 0.797 AC XY: 59268 AN XY: 74336

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.859

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.789

Alfa AF: 0.768 Hom.: 74420

Bravo AF: 0.792

Asia WGS AF: 0.823 AC: 2864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.028
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130637; hg19: chr6-31488145;