rs4257183

Variant names:

• chr15-39349137-C-T
• rs4257183
• ENST00000558209.1:n.451+10652G>A

Variant summary

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

The ENST00000558209.1(ENSG00000259345):​n.451+10652G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 152,130 control chromosomes in the GnomAD database, including 49,156 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 0.80 (49156 hom., cov: 31)
• Consequence: ENSG00000259345 ENST00000558209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53
• Publications: 2 publications found

Genes affected

ENSG00000259345 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370777	XR_007064588.1	n.517+71407G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259345	ENST00000558209.1	n.451+10652G>A		intron_variant	Intron 2 of 2	3
ENSG00000259345	ENST00000559318.1	n.409-49655G>A		intron_variant	Intron 1 of 1	4
ENSG00000259345	ENST00000560484.1	n.67+71772G>A		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121630 AN: 152012 Hom.: 49129 Cov.: 31

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.800 AC: 121707 AN: 152130 Hom.: 49156 Cov.: 31 AF XY: 0.796 AC XY: 59180 AN XY: 74350

African (AFR) AF: 0.710 AC: 29460 AN: 41470

American (AMR) AF: 0.710 AC: 10855 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2990 AN: 3472

East Asian (EAS) AF: 0.654 AC: 3385 AN: 5172

South Asian (SAS) AF: 0.798 AC: 3840 AN: 4810

European-Finnish (FIN) AF: 0.843 AC: 8932 AN: 10592

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59417 AN: 68006

Other (OTH) AF: 0.811 AC: 1715 AN: 2114

Alfa AF: 0.851 Hom.: 28016

Bravo AF: 0.782

Asia WGS AF: 0.733 AC: 2548 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.014
DANN	Benign	0.71
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs4257183; hg19: chr15-39641338;