rs10431538

Variant names:

• chr12-51925076-G-A
• rs10431538

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.152 in 152,166 control chromosomes in the GnomAD database, including 2,544 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 0.15 (2544 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.92

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 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: 0.152 AC: 23167 AN: 152048 Hom.: 2543 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0958

Gnomad SAS AF: 0.0665

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0860

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.152 AC: 23185 AN: 152166 Hom.: 2544 Cov.: 32 AF XY: 0.150 AC XY: 11154 AN XY: 74400

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.0958

Gnomad4 SAS AF: 0.0668

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.0860

Gnomad4 OTH AF: 0.139

Alfa AF: 0.101 Hom.: 1371

Bravo AF: 0.162

Asia WGS AF: 0.107 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	23
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10431538; hg19: chr12-52318860;