rs156658

Variant names:

• chr15-39243175-G-A
• rs156658
• ENST00000558209.1:n.451+116614C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-39243175-G-A
• chr15-39243175-G-C
• chr15-39243175-G-T

Variant summary

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

The ENST00000558209.1(ENSG00000259345):​n.451+116614C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 152,060 control chromosomes in the GnomAD database, including 57,703 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 0.87 (57703 hom., cov: 31)
• Consequence: ENSG00000259345 ENST00000558209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 7 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 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+116614C>T		intron	N/A
	ENSG00000259345	ENST00000560484.1	TSL:4	n.68-171567C>T		intron	N/A
	ENSG00000259345	ENST00000561058.5	TSL:4	n.44+30665C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.869 AC: 132098 AN: 151942 Hom.: 57673 Cov.: 31

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.869 AC: 132187 AN: 152060 Hom.: 57703 Cov.: 31 AF XY: 0.874 AC XY: 64955 AN XY: 74308

African (AFR) AF: 0.783 AC: 32460 AN: 41474

American (AMR) AF: 0.917 AC: 13998 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3156 AN: 3468

East Asian (EAS) AF: 0.988 AC: 5088 AN: 5148

South Asian (SAS) AF: 0.887 AC: 4266 AN: 4812

European-Finnish (FIN) AF: 0.926 AC: 9825 AN: 10606

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

European-Non Finnish (NFE) AF: 0.892 AC: 60604 AN: 67972

Other (OTH) AF: 0.862 AC: 1818 AN: 2108

Alfa AF: 0.886 Hom.: 97617

Bravo AF: 0.862

Asia WGS AF: 0.899 AC: 3127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.62
PhyloP100		0.021

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs156658;

hg19: chr15-39535376;