rs12779790

Positions:

• chr10-12286011-A-G

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 0.169 in 151,540 control chromosomes in the GnomAD database, including 2,236 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 0.17 (2236 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 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: 0.169 AC: 25564 AN: 151424 Hom.: 2231 Cov.: 31

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.169 AC: 25587 AN: 151540 Hom.: 2236 Cov.: 31 AF XY: 0.169 AC XY: 12476 AN XY: 73990

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.170

Alfa AF: 0.172 Hom.: 376

Bravo AF: 0.164

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12779790; hg19: chr10-12328010;