rs931567

chr3-31394085-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;