rs2010851

Variant names:

• chr12-1647476-C-A
• rs2010851

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;