rs10745813

chr12-97871686-G-A

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 0.8 in 152,072 control chromosomes in the GnomAD database, including 49,320 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 0.80 (49320 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 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: 0.799 AC: 121478 AN: 151954 Hom.: 49272 Cov.: 31

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.800 AC: 121585 AN: 152072 Hom.: 49320 Cov.: 31 AF XY: 0.789 AC XY: 58635 AN XY: 74310

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.826

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.814

Alfa AF: 0.809 Hom.: 11435

Bravo AF: 0.819

Asia WGS AF: 0.528 AC: 1839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.31
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10745813; hg19: chr12-98265464;