15-29439240-G-A

Variant names:

• chr15-29439240-G-A
• rs11856574
• NM_015307.2:c.220-57409C>T

Variant summary

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

The NM_015307.2(ENTREP2):​c.220-57409C>T 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 149,694 control chromosomes in the GnomAD database, including 2,387 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 (2387 hom., cov: 29)
• Consequence: ENTREP2 NM_015307.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 5 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.333 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.220-57409C>T		intron	N/A	NP_056122.1
	ENTREP2	NM_001387214.1		c.220-57409C>T		intron	N/A	NP_001374143.1
	ENTREP2	NM_001387215.1		c.-69-57409C>T		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.220-57409C>T		intron	N/A	ENSP00000261275.4
	ENTREP2	ENST00000560082.1	TSL:4	c.-70+13330C>T		intron	N/A	ENSP00000452860.1
	ENTREP2	ENST00000560050.1	TSL:4	n.484-57409C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25620 AN: 149574 Hom.: 2386 Cov.: 29

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.0962

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.171 AC: 25645 AN: 149694 Hom.: 2387 Cov.: 29 AF XY: 0.177 AC XY: 12893 AN XY: 72882

African (AFR) AF: 0.200 AC: 8095 AN: 40556

American (AMR) AF: 0.171 AC: 2567 AN: 14984

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3454

East Asian (EAS) AF: 0.347 AC: 1734 AN: 5002

South Asian (SAS) AF: 0.184 AC: 857 AN: 4658

European-Finnish (FIN) AF: 0.190 AC: 1915 AN: 10096

Middle Eastern (MID) AF: 0.0966 AC: 28 AN: 290

European-Non Finnish (NFE) AF: 0.139 AC: 9419 AN: 67662

Other (OTH) AF: 0.160 AC: 333 AN: 2084

Alfa AF: 0.151 Hom.: 5651

Bravo AF: 0.171

Asia WGS AF: 0.250 AC: 860 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.0
DANN	Benign	0.85
PhyloP100		0.25
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: rs11856574; hg19: chr15-29731444;