rs2010851

Positions:

• chr12-1647476-C-A
• chr12-1647476-C-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 0.674 in 152,006 control chromosomes in the GnomAD database, including 34,634 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 0.67 (34634 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.650

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102361 AN: 151888 Hom.: 34623 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.674 AC: 102424 AN: 152006 Hom.: 34634 Cov.: 32 AF XY: 0.677 AC XY: 50343 AN XY: 74318

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.654

Alfa AF: 0.679 Hom.: 54508

Bravo AF: 0.665

Asia WGS AF: 0.675 AC: 2349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2010851; hg19: chr12-1756642;