chr12-10353570-A-G

Position:

• chr12-10353570-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 0.462 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;