15-29338995-T-C

Variant names:

• chr15-29338995-T-C
• rs846561
• NM_015307.2:c.276+42780A>G

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+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
• Publications: 1 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=-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 rank	MANE	Protein	UniProt
ENTREP2	NM_015307.2	c.276+42780A>G		intron_variant	Intron 2 of 10	ENST00000261275.5	NP_056122.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTREP2	ENST00000261275.5	c.276+42780A>G		intron_variant	Intron 2 of 10	5	NM_015307.2	ENSP00000261275.4
ENTREP2	ENST00000560082.1	c.-13+42780A>G		intron_variant	Intron 2 of 3	4		ENSP00000452860.1

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

African (AFR) AF: 0.808 AC: 33543 AN: 41508

American (AMR) AF: 0.784 AC: 11988 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.891 AC: 3091 AN: 3468

East Asian (EAS) AF: 0.721 AC: 3706 AN: 5142

South Asian (SAS) AF: 0.746 AC: 3595 AN: 4822

European-Finnish (FIN) AF: 0.753 AC: 7973 AN: 10588

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.800 AC: 54397 AN: 67992

Other (OTH) AF: 0.815 AC: 1719 AN: 2110

Alfa AF: 0.782 Hom.: 10733

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
PhyloP100		-1.8
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: rs846561; hg19: chr15-29631199;