12-10353570-A-G

Variant names:

• chr12-10353570-A-G
• rs10772266

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 0.462 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.462 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

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.422

Alfa AF: 0.406 Hom.: 1905

Bravo AF: 0.470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10772266; hg19: chr12-10506169;