rs12778642

Variant names:

• chr10-92704550-G-T
• rs12778642

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;