rs817957

chr15-29330596-C-Achr15-29330596-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ENTREP2	NM_015307.2	c.276+51179G>T		intron_variant		ENST00000261275.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENTREP2	ENST00000261275.5	c.276+51179G>T		intron_variant		5	NM_015307.2	P1
ENTREP2	ENST00000560082.1	c.-13+51179G>T		intron_variant		4

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

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.287

Alfa AF: 0.198 Hom.: 4531

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs817957; hg19: chr15-29622800;