12-107145708-C-T

Variant names:

• chr12-107145708-C-T
• rs1921120

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.662 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

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.942

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.655

Alfa AF: 0.653 Hom.: 16174

Bravo AF: 0.662

Asia WGS AF: 0.763 AC: 2654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1921120; hg19: chr12-107539486;