rs931567

Variant names:

• chr3-31394085-G-A
• rs931567

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 0.358 in 151,922 control chromosomes in the GnomAD database, including 13,743 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 0.36 (13743 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.699 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: 0.358 AC: 54285 AN: 151804 Hom.: 13702 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.358 AC: 54371 AN: 151922 Hom.: 13743 Cov.: 32 AF XY: 0.355 AC XY: 26350 AN XY: 74242

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.321

Alfa AF: 0.234 Hom.: 3194

Bravo AF: 0.387

Asia WGS AF: 0.436 AC: 1518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs931567; hg19: chr3-31435577;