15-29338995-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015307.2(ENTREP2):c.276+42780A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 152,116 control chromosomes in the GnomAD database, including 48,252 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 0.80 (48252 hom., cov: 32)
• Consequence: ENTREP2 NM_015307.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENTREP2	NM_015307.2	c.276+42780A>G		intron_variant		ENST00000261275.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENTREP2	ENST00000261275.5	c.276+42780A>G		intron_variant		5	NM_015307.2	P1
ENTREP2	ENST00000560082.1	c.-13+42780A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120896 AN: 151996 Hom.: 48221 Cov.: 32

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.795 AC: 120977 AN: 152116 Hom.: 48252 Cov.: 32 AF XY: 0.793 AC XY: 58991 AN XY: 74350

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.891

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.800

Gnomad4 OTH AF: 0.815

Alfa AF: 0.742 Hom.: 2521

Bravo AF: 0.802

Asia WGS AF: 0.709 AC: 2464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.22
Dann	Benign	0.34

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: rs846561; hg19: chr15-29631199;