12-2951058-A-C

Variant names:

• chr12-2951058-A-C
• rs10774085

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 0.428 in 151,184 control chromosomes in the GnomAD database, including 15,223 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 0.43 (15223 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 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: 0.428 AC: 64652 AN: 151078 Hom.: 15180 Cov.: 29

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.428 AC: 64753 AN: 151184 Hom.: 15223 Cov.: 29 AF XY: 0.425 AC XY: 31389 AN XY: 73816

African (AFR) AF: 0.638 AC: 26186 AN: 41014

American (AMR) AF: 0.385 AC: 5836 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1555 AN: 3472

East Asian (EAS) AF: 0.475 AC: 2443 AN: 5138

South Asian (SAS) AF: 0.393 AC: 1881 AN: 4792

European-Finnish (FIN) AF: 0.331 AC: 3442 AN: 10404

Middle Eastern (MID) AF: 0.385 AC: 111 AN: 288

European-Non Finnish (NFE) AF: 0.324 AC: 21975 AN: 67906

Other (OTH) AF: 0.430 AC: 903 AN: 2102

Alfa AF: 0.362 Hom.: 46604

Bravo AF: 0.444

Asia WGS AF: 0.473 AC: 1643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.28
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10774085; hg19: chr12-3060224;