rs1520942

chr15-29361793-G-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+19982C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,132 control chromosomes in the GnomAD database, including 2,425 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 0.17 (2425 hom., cov: 32)
• Consequence: ENTREP2 NM_015307.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENTREP2	NM_015307.2	c.276+19982C>A		intron_variant		ENST00000261275.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENTREP2	ENST00000261275.5	c.276+19982C>A		intron_variant		5	NM_015307.2	P1
ENTREP2	ENST00000560082.1	c.-13+19982C>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25945 AN: 152014 Hom.: 2425 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.171 AC: 25959 AN: 152132 Hom.: 2425 Cov.: 32 AF XY: 0.172 AC XY: 12764 AN XY: 74380

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.159

Alfa AF: 0.156 Hom.: 3304

Bravo AF: 0.166

Asia WGS AF: 0.309 AC: 1074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.39
Dann	Benign	0.48

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: rs1520942; hg19: chr15-29653997;