rs12781751

chr10-31583898-C-T

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/exons	MANE	UniProt

Ensembl

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