12-28003148-C-G

Variant names:

• chr12-28003148-C-G
• rs12371778

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 0.089 in 151,514 control chromosomes in the GnomAD database, including 707 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 0.089 (707 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 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: 0.0891 AC: 13484 AN: 151410 Hom.: 707 Cov.: 29

Gnomad AFR AF: 0.0382

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0816

Gnomad ASJ AF: 0.0921

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0678

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0833

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

GnomAD4 genome AF: 0.0890 AC: 13483 AN: 151514 Hom.: 707 Cov.: 29 AF XY: 0.0868 AC XY: 6425 AN XY: 74036

African (AFR) AF: 0.0382 AC: 1577 AN: 41286

American (AMR) AF: 0.0813 AC: 1238 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.0921 AC: 319 AN: 3464

East Asian (EAS) AF: 0.190 AC: 978 AN: 5134

South Asian (SAS) AF: 0.129 AC: 615 AN: 4766

European-Finnish (FIN) AF: 0.0678 AC: 712 AN: 10498

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7728 AN: 67852

Other (OTH) AF: 0.0829 AC: 173 AN: 2088

Alfa AF: 0.0421 Hom.: 43

Bravo AF: 0.0892

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.33
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs12371778; hg19: chr12-28156081;