chr12-52804344-T-C

Variant names:

• chr12-52804344-T-C
• rs7134792

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 0.845 in 152,160 control chromosomes in the GnomAD database, including 54,745 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 0.85 (54745 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 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: 0.845 AC: 128489 AN: 152042 Hom.: 54696 Cov.: 31

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.845 AC: 128595 AN: 152160 Hom.: 54745 Cov.: 31 AF XY: 0.840 AC XY: 62489 AN XY: 74386

African (AFR) AF: 0.937 AC: 38910 AN: 41524

American (AMR) AF: 0.787 AC: 12031 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2856 AN: 3472

East Asian (EAS) AF: 0.916 AC: 4738 AN: 5174

South Asian (SAS) AF: 0.654 AC: 3140 AN: 4800

European-Finnish (FIN) AF: 0.848 AC: 8982 AN: 10592

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.812 AC: 55227 AN: 67990

Other (OTH) AF: 0.819 AC: 1732 AN: 2114

Alfa AF: 0.814 Hom.: 35262

Bravo AF: 0.852

Asia WGS AF: 0.767 AC: 2669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.35
DANN	Benign	0.36
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs7134792; hg19: chr12-53198128;