12-107145708-C-T

Variant names:

• chr12-107145708-C-T
• rs1921120

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 0.662 in 152,108 control chromosomes in the GnomAD database, including 33,594 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 0.66 (33594 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100650 AN: 151990 Hom.: 33549 Cov.: 33

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.662 AC: 100752 AN: 152108 Hom.: 33594 Cov.: 33 AF XY: 0.667 AC XY: 49591 AN XY: 74376

African (AFR) AF: 0.639 AC: 26516 AN: 41476

American (AMR) AF: 0.669 AC: 10221 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2013 AN: 3468

East Asian (EAS) AF: 0.942 AC: 4885 AN: 5186

South Asian (SAS) AF: 0.643 AC: 3101 AN: 4826

European-Finnish (FIN) AF: 0.674 AC: 7140 AN: 10592

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44817 AN: 67970

Other (OTH) AF: 0.655 AC: 1382 AN: 2110

Alfa AF: 0.653 Hom.: 18005

Bravo AF: 0.662

Asia WGS AF: 0.763 AC: 2654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.41
DANN	Benign	0.40
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1921120; hg19: chr12-107539486;