15-29658588-C-G

Variant names:

• chr15-29658588-C-G
• rs1459359
• NM_001387215.1:c.-70+16511G>C

Variant summary

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

The NM_001387215.1(ENTREP2):​c.-70+16511G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 151,848 control chromosomes in the GnomAD database, including 5,746 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 0.21 (5746 hom., cov: 32)
• Consequence: ENTREP2 NM_001387215.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 2 publications found

Genes affected

ENTREP2 (HGNC:29075): (endosomal transmembrane epsin interactor 2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTREP2	NM_001387215.1	c.-70+16511G>C		intron_variant	Intron 1 of 11		NP_001374144.1
ENTREP2	NM_001387216.1	c.-70+16511G>C		intron_variant	Intron 1 of 10		NP_001374145.1
ENTREP2	NM_001387217.1	c.-70+16511G>C		intron_variant	Intron 1 of 10		NP_001374146.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31753 AN: 151734 Hom.: 5704 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0645

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0950

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.210 AC: 31863 AN: 151848 Hom.: 5746 Cov.: 32 AF XY: 0.207 AC XY: 15378 AN XY: 74192

African (AFR) AF: 0.493 AC: 20401 AN: 41364

American (AMR) AF: 0.138 AC: 2106 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0645 AC: 224 AN: 3472

East Asian (EAS) AF: 0.111 AC: 573 AN: 5168

South Asian (SAS) AF: 0.163 AC: 782 AN: 4804

European-Finnish (FIN) AF: 0.0733 AC: 770 AN: 10504

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0950 AC: 6456 AN: 67944

Other (OTH) AF: 0.188 AC: 397 AN: 2112

Alfa AF: 0.0708 Hom.: 119

Bravo AF: 0.228

Asia WGS AF: 0.179 AC: 620 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.33
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs1459359; hg19: chr15-29950792;