chr15-29259260-A-G

Variant names:

• chr15-29259260-A-G
• rs509639
• NM_015307.2:c.277-6782T>C

Variant summary

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

The NM_015307.2(ENTREP2):​c.277-6782T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 152,122 control chromosomes in the GnomAD database, including 27,235 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 0.60 (27235 hom., cov: 33)
• Consequence: ENTREP2 NM_015307.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.617 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTREP2	NM_015307.2	MANE Select	c.277-6782T>C		intron	N/A	NP_056122.1
	ENTREP2	NM_001387214.1		c.277-6782T>C		intron	N/A	NP_001374143.1
	ENTREP2	NM_001387215.1		c.-12-6782T>C		intron	N/A	NP_001374144.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTREP2	ENST00000261275.5	TSL:5 MANE Select	c.277-6782T>C		intron	N/A	ENSP00000261275.4
	ENTREP2	ENST00000560082.1	TSL:4	c.-12-6782T>C		intron	N/A	ENSP00000452860.1

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90919 AN: 152004 Hom.: 27214 Cov.: 33

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.598 AC: 90992 AN: 152122 Hom.: 27235 Cov.: 33 AF XY: 0.595 AC XY: 44236 AN XY: 74378

African (AFR) AF: 0.592 AC: 24581 AN: 41492

American (AMR) AF: 0.562 AC: 8595 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1892 AN: 3472

East Asian (EAS) AF: 0.602 AC: 3121 AN: 5182

South Asian (SAS) AF: 0.636 AC: 3066 AN: 4822

European-Finnish (FIN) AF: 0.569 AC: 6013 AN: 10574

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41786 AN: 67966

Other (OTH) AF: 0.593 AC: 1253 AN: 2112

Alfa AF: 0.598 Hom.: 5366

Bravo AF: 0.593

Asia WGS AF: 0.609 AC: 2117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.55
PhyloP100		-0.072
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: rs509639; hg19: chr15-29551464;