12-58009467-C-G

Variant names:

• chr12-58009467-C-G
• rs7304755

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 0.614 in 152,062 control chromosomes in the GnomAD database, including 29,766 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 0.61 (29766 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.696 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: 0.615 AC: 93401 AN: 151944 Hom.: 29772 Cov.: 33

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.614 AC: 93414 AN: 152062 Hom.: 29766 Cov.: 33 AF XY: 0.612 AC XY: 45510 AN XY: 74312

African (AFR) AF: 0.475 AC: 19706 AN: 41452

American (AMR) AF: 0.601 AC: 9179 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2749 AN: 3472

East Asian (EAS) AF: 0.320 AC: 1659 AN: 5182

South Asian (SAS) AF: 0.713 AC: 3430 AN: 4812

European-Finnish (FIN) AF: 0.641 AC: 6766 AN: 10562

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.702 AC: 47701 AN: 67998

Other (OTH) AF: 0.678 AC: 1434 AN: 2114

Alfa AF: 0.548 Hom.: 1637

Bravo AF: 0.601

Asia WGS AF: 0.515 AC: 1793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.7
DANN	Benign	0.66
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs7304755; hg19: chr12-58403250;