12-53243682-C-T

Variant names:

• chr12-53243682-C-T
• rs7314769

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 0.587 in 151,932 control chromosomes in the GnomAD database, including 26,582 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 0.59 (26582 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298
• Publications: 15 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 (EAS) allele frequency at 95% confidence interval = 0.793 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: 0.587 AC: 89068 AN: 151814 Hom.: 26548 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.587 AC: 89158 AN: 151932 Hom.: 26582 Cov.: 31 AF XY: 0.589 AC XY: 43715 AN XY: 74258

African (AFR) AF: 0.604 AC: 25011 AN: 41432

American (AMR) AF: 0.607 AC: 9263 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1904 AN: 3470

East Asian (EAS) AF: 0.813 AC: 4192 AN: 5154

South Asian (SAS) AF: 0.749 AC: 3603 AN: 4812

European-Finnish (FIN) AF: 0.529 AC: 5577 AN: 10550

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37766 AN: 67930

Other (OTH) AF: 0.592 AC: 1247 AN: 2108

Alfa AF: 0.568 Hom.: 44221

Bravo AF: 0.594

Asia WGS AF: 0.732 AC: 2547 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	5.1
DANN	Benign	0.51
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs7314769; hg19: chr12-53637466;