rs10774085

Variant names:

• chr12-2951058-A-C
• rs10774085

Your query was ambiguous. Multiple possible variants found:

• chr12-2951058-A-C
• chr12-2951058-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 0.428 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.430

Alfa AF: 0.347 Hom.: 19136

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10774085; hg19: chr12-3060224;