ENST00000558209.1:n.452-128458A>G

Variant names:

• chr15-39200066-T-C
• rs10520122
• ENST00000558209.1:n.452-128458A>G

Variant summary

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

The ENST00000558209.1(ENSG00000259345):​n.452-128458A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,230 control chromosomes in the GnomAD database, including 1,562 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 0.13 (1562 hom., cov: 32)
• Consequence: ENSG00000259345 ENST00000558209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.746
• Publications: 6 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=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370777	XR_007064588.1	n.518-128458A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259345	ENST00000558209.1	n.452-128458A>G		intron_variant	Intron 2 of 2	3
ENSG00000259345	ENST00000560484.1	n.68-128458A>G		intron_variant	Intron 1 of 3	4
ENSG00000259345	ENST00000561058.5	n.44+73774A>G		intron_variant	Intron 1 of 5	4

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19829 AN: 152112 Hom.: 1563 Cov.: 32

Gnomad AFR AF: 0.0417

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.130 AC: 19834 AN: 152230 Hom.: 1562 Cov.: 32 AF XY: 0.131 AC XY: 9780 AN XY: 74426

African (AFR) AF: 0.0418 AC: 1736 AN: 41562

American (AMR) AF: 0.158 AC: 2407 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3470

East Asian (EAS) AF: 0.160 AC: 831 AN: 5178

South Asian (SAS) AF: 0.166 AC: 799 AN: 4816

European-Finnish (FIN) AF: 0.129 AC: 1371 AN: 10602

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11312 AN: 68000

Other (OTH) AF: 0.166 AC: 351 AN: 2114

Alfa AF: 0.157 Hom.: 5807

Bravo AF: 0.126

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	14
DANN	Benign	0.88
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs10520122; hg19: chr15-39492267;