rs12778642

chr10-92704550-G-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 0.448 in 151,846 control chromosomes in the GnomAD database, including 15,608 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 0.45 (15608 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 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: 0.448 AC: 67969 AN: 151728 Hom.: 15601 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.448 AC: 68013 AN: 151846 Hom.: 15608 Cov.: 31 AF XY: 0.451 AC XY: 33430 AN XY: 74196

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.433

Alfa AF: 0.432 Hom.: 19038

Bravo AF: 0.440

Asia WGS AF: 0.619 AC: 2151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.76
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12778642; hg19: chr10-94464307;