chr15-48098759-C-T

Variant names:

• chr15-48098759-C-T
• rs12441154

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 0.19 in 152,190 control chromosomes in the GnomAD database, including 7,048 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 0.19 (7048 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

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 = 0.875 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: 0.189 AC: 28796 AN: 152072 Hom.: 7019 Cov.: 33

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.00374

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.0142

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00707

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.190 AC: 28878 AN: 152190 Hom.: 7048 Cov.: 33 AF XY: 0.194 AC XY: 14408 AN XY: 74410

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.00374

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.0142

Gnomad4 NFE AF: 0.00707

Gnomad4 OTH AF: 0.170

Alfa AF: 0.157 Hom.: 688

Bravo AF: 0.222

Asia WGS AF: 0.606 AC: 2106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12441154; hg19: chr15-48390956;