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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;