ENST00000558209.1:n.451+103663T>C

Variant names:

• chr15-39256126-A-G
• rs156787
• ENST00000558209.1:n.451+103663T>C

Variant summary

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

The ENST00000558209.1(ENSG00000259345):​n.451+103663T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 151,952 control chromosomes in the GnomAD database, including 55,494 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 0.85 (55494 hom., cov: 31)
• Consequence: ENSG00000259345 ENST00000558209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.517
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558209.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259345	ENST00000558209.1	TSL:3	n.451+103663T>C		intron	N/A
	ENSG00000259345	ENST00000560484.1	TSL:4	n.67+164783T>C		intron	N/A
	ENSG00000259345	ENST00000561058.5	TSL:4	n.44+17714T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129728 AN: 151834 Hom.: 55460 Cov.: 31

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.854 AC: 129816 AN: 151952 Hom.: 55494 Cov.: 31 AF XY: 0.856 AC XY: 63574 AN XY: 74254

African (AFR) AF: 0.859 AC: 35624 AN: 41458

American (AMR) AF: 0.903 AC: 13769 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2949 AN: 3468

East Asian (EAS) AF: 0.818 AC: 4203 AN: 5138

South Asian (SAS) AF: 0.837 AC: 4035 AN: 4820

European-Finnish (FIN) AF: 0.857 AC: 9070 AN: 10582

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.843 AC: 57258 AN: 67918

Other (OTH) AF: 0.854 AC: 1805 AN: 2114

Alfa AF: 0.845 Hom.: 218903

Bravo AF: 0.858

Asia WGS AF: 0.865 AC: 3012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.58
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs156787; hg19: chr15-39548327;