rs12493391

Variant names:

• chr3-31452483-A-G
• rs12493391

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 0.14 in 152,222 control chromosomes in the GnomAD database, including 1,612 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 0.14 (1612 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 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: 0.140 AC: 21309 AN: 152104 Hom.: 1609 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.140 AC: 21319 AN: 152222 Hom.: 1612 Cov.: 32 AF XY: 0.139 AC XY: 10330 AN XY: 74428

African (AFR) AF: 0.144 AC: 5998 AN: 41526

American (AMR) AF: 0.108 AC: 1648 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 740 AN: 3470

East Asian (EAS) AF: 0.112 AC: 579 AN: 5186

South Asian (SAS) AF: 0.121 AC: 582 AN: 4822

European-Finnish (FIN) AF: 0.172 AC: 1824 AN: 10590

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9385 AN: 68002

Other (OTH) AF: 0.151 AC: 320 AN: 2116

Alfa AF: 0.139 Hom.: 1648

Bravo AF: 0.137

Asia WGS AF: 0.137 AC: 477 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	9.4
DANN	Benign	0.67
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs12493391; hg19: chr3-31493975;