rs1520942

Variant names:

• chr15-29361793-G-T
• rs1520942
• NM_015307.2:c.276+19982C>A

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015307.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTREP2	NM_015307.2	MANE Select	c.276+19982C>A		intron	N/A	NP_056122.1	O60320-1
	ENTREP2	NM_001387214.1		c.276+19982C>A		intron	N/A	NP_001374143.1
	ENTREP2	NM_001387215.1		c.-13+19982C>A		intron	N/A	NP_001374144.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTREP2	ENST00000261275.5	TSL:5 MANE Select	c.276+19982C>A		intron	N/A	ENSP00000261275.4	O60320-1
	ENTREP2	ENST00000918355.1		c.276+19982C>A		intron	N/A	ENSP00000588414.1
	ENTREP2	ENST00000910616.1		c.276+19982C>A		intron	N/A	ENSP00000580675.1

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

African (AFR) AF: 0.177 AC: 7350 AN: 41512

American (AMR) AF: 0.142 AC: 2170 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 359 AN: 3472

East Asian (EAS) AF: 0.377 AC: 1942 AN: 5154

South Asian (SAS) AF: 0.266 AC: 1279 AN: 4812

European-Finnish (FIN) AF: 0.159 AC: 1683 AN: 10590

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.157 AC: 10682 AN: 67984

Other (OTH) AF: 0.159 AC: 336 AN: 2108

Alfa AF: 0.159 Hom.: 7734

Bravo AF: 0.166

Asia WGS AF: 0.309 AC: 1074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.39
DANN	Benign	0.48
PhyloP100		-0.36
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: rs1520942; hg19: chr15-29653997;