15-29259260-A-G

Position:

• chr15-29259260-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTREP2	NM_015307.2	c.277-6782T>C		intron_variant		ENST00000261275.5	NP_056122.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTREP2	ENST00000261275.5	c.277-6782T>C		intron_variant		5	NM_015307.2	ENSP00000261275.4
ENTREP2	ENST00000560082.1	c.-12-6782T>C		intron_variant		4		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

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.593

Alfa AF: 0.599 Hom.: 5243

Bravo AF: 0.593

Asia WGS AF: 0.609 AC: 2117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.55

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: rs509639; hg19: chr15-29551464;