12-90166301-C-T

Variant names:

• chr12-90166301-C-T
• rs2579088

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 0.642 in 151,984 control chromosomes in the GnomAD database, including 32,271 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 (32271 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.754 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: 0.643 AC: 97601 AN: 151866 Hom.: 32271 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.642 AC: 97628 AN: 151984 Hom.: 32271 Cov.: 32 AF XY: 0.643 AC XY: 47775 AN XY: 74302

African (AFR) AF: 0.486 AC: 20126 AN: 41418

American (AMR) AF: 0.541 AC: 8243 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2693 AN: 3468

East Asian (EAS) AF: 0.769 AC: 3971 AN: 5164

South Asian (SAS) AF: 0.774 AC: 3735 AN: 4824

European-Finnish (FIN) AF: 0.698 AC: 7387 AN: 10582

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49255 AN: 67972

Other (OTH) AF: 0.643 AC: 1360 AN: 2114

Alfa AF: 0.696 Hom.: 104764

Bravo AF: 0.619

Asia WGS AF: 0.707 AC: 2461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	15
DANN	Benign	0.66
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2579088; hg19: chr12-90560078;