12-107279425-T-G

Variant names:

• chr12-107279425-T-G
• rs2374688

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 0.637 in 152,020 control chromosomes in the GnomAD database, including 31,315 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 0.64 (31315 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96738 AN: 151902 Hom.: 31258 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.637 AC: 96869 AN: 152020 Hom.: 31315 Cov.: 32 AF XY: 0.639 AC XY: 47522 AN XY: 74314

African (AFR) AF: 0.714 AC: 29579 AN: 41432

American (AMR) AF: 0.665 AC: 10154 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1869 AN: 3468

East Asian (EAS) AF: 0.781 AC: 4044 AN: 5176

South Asian (SAS) AF: 0.594 AC: 2855 AN: 4810

European-Finnish (FIN) AF: 0.589 AC: 6228 AN: 10580

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.588 AC: 39959 AN: 67978

Other (OTH) AF: 0.628 AC: 1328 AN: 2116

Alfa AF: 0.597 Hom.: 13315

Bravo AF: 0.649

Asia WGS AF: 0.715 AC: 2480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.77
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2374688; hg19: chr12-107673202;