12-90173201-C-T

Position:

• chr12-90173201-C-T

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 0.807 in 151,934 control chromosomes in the GnomAD database, including 49,708 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 0.81 (49708 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122593 AN: 151816 Hom.: 49669 Cov.: 31

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.807 AC: 122684 AN: 151934 Hom.: 49708 Cov.: 31 AF XY: 0.810 AC XY: 60138 AN XY: 74252

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.780

Gnomad4 OTH AF: 0.793

Alfa AF: 0.792 Hom.: 23846

Bravo AF: 0.802

Asia WGS AF: 0.810 AC: 2818 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.066
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1347851; hg19: chr12-90566978;