12-73376014-T-C

Variant names:

• chr12-73376014-T-C
• rs10785024

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 0.559 in 151,862 control chromosomes in the GnomAD database, including 24,166 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 0.56 (24166 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.748 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: 0.559 AC: 84823 AN: 151744 Hom.: 24163 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.559 AC: 84853 AN: 151862 Hom.: 24166 Cov.: 31 AF XY: 0.557 AC XY: 41377 AN XY: 74226

African (AFR) AF: 0.453 AC: 18768 AN: 41432

American (AMR) AF: 0.559 AC: 8509 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1934 AN: 3464

East Asian (EAS) AF: 0.768 AC: 3961 AN: 5156

South Asian (SAS) AF: 0.612 AC: 2948 AN: 4816

European-Finnish (FIN) AF: 0.533 AC: 5622 AN: 10556

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41143 AN: 67896

Other (OTH) AF: 0.598 AC: 1262 AN: 2112

Alfa AF: 0.591 Hom.: 15490

Bravo AF: 0.555

Asia WGS AF: 0.669 AC: 2322 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.71
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs10785024; hg19: chr12-73769794;