rs10431538

Positions:

• chr12-51925076-G-A

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/exons	MANE	UniProt

Ensembl

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