12-15021655-C-T

Variant names:

• chr12-15021655-C-T
• rs2445402

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 0.785 in 151,876 control chromosomes in the GnomAD database, including 47,008 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 0.79 (47008 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.818 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: 0.785 AC: 119166 AN: 151758 Hom.: 46972 Cov.: 30

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.785 AC: 119255 AN: 151876 Hom.: 47008 Cov.: 30 AF XY: 0.779 AC XY: 57779 AN XY: 74216

African (AFR) AF: 0.792 AC: 32814 AN: 41428

American (AMR) AF: 0.687 AC: 10468 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2420 AN: 3470

East Asian (EAS) AF: 0.700 AC: 3594 AN: 5134

South Asian (SAS) AF: 0.679 AC: 3261 AN: 4806

European-Finnish (FIN) AF: 0.777 AC: 8211 AN: 10562

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.824 AC: 55982 AN: 67926

Other (OTH) AF: 0.753 AC: 1588 AN: 2110

Alfa AF: 0.804 Hom.: 151573

Bravo AF: 0.777

Asia WGS AF: 0.674 AC: 2341 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.93
DANN	Benign	0.46
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs2445402; hg19: chr12-15174589;