rs12441154

chr15-48098759-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 0.19 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;