12-125719508-T-C

Variant names:

• chr12-125719508-T-C
• rs10492036

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 0.632 in 152,034 control chromosomes in the GnomAD database, including 30,670 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 0.63 (30670 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 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: 0.632 AC: 95962 AN: 151916 Hom.: 30641 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.632 AC: 96051 AN: 152034 Hom.: 30670 Cov.: 32 AF XY: 0.631 AC XY: 46876 AN XY: 74320

African (AFR) AF: 0.618 AC: 25607 AN: 41460

American (AMR) AF: 0.734 AC: 11214 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2254 AN: 3472

East Asian (EAS) AF: 0.885 AC: 4565 AN: 5160

South Asian (SAS) AF: 0.595 AC: 2868 AN: 4822

European-Finnish (FIN) AF: 0.540 AC: 5710 AN: 10566

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41480 AN: 67956

Other (OTH) AF: 0.660 AC: 1396 AN: 2116

Alfa AF: 0.592 Hom.: 12238

Bravo AF: 0.653

Asia WGS AF: 0.702 AC: 2443 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	1.4
DANN	Benign	0.35
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs10492036; hg19: chr12-126204054;