10-12286011-A-G

Variant names:

• chr10-12286011-A-G
• rs12779790

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 221 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.146 AC: 6014 AN: 41314

American (AMR) AF: 0.161 AC: 2446 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3468

East Asian (EAS) AF: 0.183 AC: 932 AN: 5106

South Asian (SAS) AF: 0.142 AC: 683 AN: 4806

European-Finnish (FIN) AF: 0.214 AC: 2241 AN: 10474

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12060 AN: 67904

Other (OTH) AF: 0.170 AC: 357 AN: 2094

Alfa AF: 0.169 Hom.: 418

Bravo AF: 0.164

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.25
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs12779790; hg19: chr10-12328010;