rs11856574

chr15-29439240-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENTREP2	NM_015307.2	c.220-57409C>T		intron_variant		ENST00000261275.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENTREP2	ENST00000261275.5	c.220-57409C>T		intron_variant		5	NM_015307.2	P1
ENTREP2	ENST00000560082.1	c.-70+13330C>T		intron_variant		4
ENTREP2	ENST00000560050.1	n.484-57409C>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.160

Alfa AF: 0.146 Hom.: 2119

Bravo AF: 0.171

Asia WGS AF: 0.250 AC: 860 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.0
Dann	Benign	0.85

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: rs11856574; hg19: chr15-29731444;