rs12441154

Variant names:

• chr15-48098759-C-T
• rs12441154
• ENST00000730753.1:n.65-9856C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000730753.1(ENSG00000295542):​n.65-9856C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000295542 ENST00000730753.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 2 publications found

Genes affected

ENSG00000295542 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000295542	ENST00000730753.1	n.65-9856C>T		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.451 AC: 18698 AN: 41476

American (AMR) AF: 0.230 AC: 3524 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00374 AC: 13 AN: 3472

East Asian (EAS) AF: 0.896 AC: 4625 AN: 5160

South Asian (SAS) AF: 0.212 AC: 1024 AN: 4828

European-Finnish (FIN) AF: 0.0142 AC: 151 AN: 10620

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00707 AC: 481 AN: 68020

Other (OTH) AF: 0.170 AC: 359 AN: 2112

Alfa AF: 0.115 Hom.: 1014

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
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs12441154; hg19: chr15-48390956;