rs12781751

Variant names:

• chr10-31583898-C-T
• rs12781751

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 0.512 in 152,064 control chromosomes in the GnomAD database, including 20,131 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 0.51 (20131 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.566 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: 0.512 AC: 77834 AN: 151946 Hom.: 20102 Cov.: 33

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.512 AC: 77912 AN: 152064 Hom.: 20131 Cov.: 33 AF XY: 0.505 AC XY: 37564 AN XY: 74312

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.502

Alfa AF: 0.535 Hom.: 28705

Bravo AF: 0.528

Asia WGS AF: 0.383 AC: 1335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12781751; hg19: chr10-31872826;