12-42613594-T-C

Variant names:

• chr12-42613594-T-C
• rs7964774

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 0.838 in 152,040 control chromosomes in the GnomAD database, including 55,421 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 0.84 (55421 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.944 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: 0.839 AC: 127398 AN: 151922 Hom.: 55401 Cov.: 31

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.954

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.950

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.838 AC: 127458 AN: 152040 Hom.: 55421 Cov.: 31 AF XY: 0.841 AC XY: 62494 AN XY: 74306

African (AFR) AF: 0.584 AC: 24180 AN: 41388

American (AMR) AF: 0.883 AC: 13499 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3086 AN: 3470

East Asian (EAS) AF: 0.877 AC: 4524 AN: 5156

South Asian (SAS) AF: 0.948 AC: 4558 AN: 4810

European-Finnish (FIN) AF: 0.954 AC: 10105 AN: 10590

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.950 AC: 64632 AN: 68020

Other (OTH) AF: 0.835 AC: 1758 AN: 2106

Alfa AF: 0.862 Hom.: 7068

Bravo AF: 0.823

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	11
DANN	Benign	0.68
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs7964774; hg19: chr12-43007396;