chr15-29330596-C-A

Variant names:

• chr15-29330596-C-A
• rs817957
• NM_015307.2:c.276+51179G>T

Variant summary

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

The NM_015307.2(ENTREP2):​c.276+51179G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 151,928 control chromosomes in the GnomAD database, including 9,008 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 0.30 (9008 hom., cov: 32)
• Consequence: ENTREP2 NM_015307.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTREP2	NM_015307.2	c.276+51179G>T		intron_variant	Intron 2 of 10	ENST00000261275.5	NP_056122.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTREP2	ENST00000261275.5	c.276+51179G>T		intron_variant	Intron 2 of 10	5	NM_015307.2	ENSP00000261275.4
ENTREP2	ENST00000560082.1	c.-13+51179G>T		intron_variant	Intron 2 of 3	4		ENSP00000452860.1

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45218 AN: 151810 Hom.: 8975 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.298 AC: 45299 AN: 151928 Hom.: 9008 Cov.: 32 AF XY: 0.292 AC XY: 21714 AN XY: 74248

African (AFR) AF: 0.568 AC: 23516 AN: 41408

American (AMR) AF: 0.290 AC: 4433 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 861 AN: 3468

East Asian (EAS) AF: 0.210 AC: 1086 AN: 5172

South Asian (SAS) AF: 0.172 AC: 825 AN: 4802

European-Finnish (FIN) AF: 0.143 AC: 1506 AN: 10536

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12032 AN: 67950

Other (OTH) AF: 0.287 AC: 606 AN: 2114

Alfa AF: 0.238 Hom.: 10582

Bravo AF: 0.325

Asia WGS AF: 0.191 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.40
DANN	Benign	0.39
PhyloP100		-0.56
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs817957; hg19: chr15-29622800;