12-10353570-A-G

Variant names:

• chr12-10353570-A-G
• rs10772266

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 0.462 in 150,592 control chromosomes in the GnomAD database, including 17,011 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 0.46 (17011 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.462 AC: 69584 AN: 150478 Hom.: 16995 Cov.: 30

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.462 AC: 69633 AN: 150592 Hom.: 17011 Cov.: 30 AF XY: 0.469 AC XY: 34482 AN XY: 73466

African (AFR) AF: 0.525 AC: 21570 AN: 41052

American (AMR) AF: 0.495 AC: 7500 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1450 AN: 3462

East Asian (EAS) AF: 0.904 AC: 4666 AN: 5162

South Asian (SAS) AF: 0.688 AC: 3295 AN: 4788

European-Finnish (FIN) AF: 0.371 AC: 3763 AN: 10130

Middle Eastern (MID) AF: 0.401 AC: 114 AN: 284

European-Non Finnish (NFE) AF: 0.385 AC: 26025 AN: 67558

Other (OTH) AF: 0.422 AC: 885 AN: 2098

Alfa AF: 0.410 Hom.: 2006

Bravo AF: 0.470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	8.2
DANN	Benign	0.87
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10772266; hg19: chr12-10506169;