12-76746848-T-C

Variant names:

• chr12-76746848-T-C
• rs7956544

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 0.564 in 151,842 control chromosomes in the GnomAD database, including 24,904 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 (24904 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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: 0.564 AC: 85564 AN: 151724 Hom.: 24880 Cov.: 30

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.564 AC: 85623 AN: 151842 Hom.: 24904 Cov.: 30 AF XY: 0.570 AC XY: 42303 AN XY: 74196

African (AFR) AF: 0.419 AC: 17336 AN: 41370

American (AMR) AF: 0.665 AC: 10151 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2343 AN: 3466

East Asian (EAS) AF: 0.768 AC: 3949 AN: 5142

South Asian (SAS) AF: 0.626 AC: 3014 AN: 4816

European-Finnish (FIN) AF: 0.586 AC: 6169 AN: 10526

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40667 AN: 67950

Other (OTH) AF: 0.586 AC: 1235 AN: 2106

Alfa AF: 0.579 Hom.: 6770

Bravo AF: 0.562

Asia WGS AF: 0.667 AC: 2314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.62
DANN	Benign	0.73
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs7956544; hg19: chr12-77140628;