NM_020775.5:c.153+22355T>C

Variant names:

• chr1-109136691-T-C
• rs591209
• NM_020775.5:c.153+22355T>C

Variant summary

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

The NM_020775.5(ELAPOR1):​c.153+22355T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 152,062 control chromosomes in the GnomAD database, including 27,616 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 0.58 (27616 hom., cov: 32)
• Consequence: ELAPOR1 NM_020775.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.87
• Publications: 0 publications found

Genes affected

ELAPOR1 (HGNC:29618): (endosome-lysosome associated apoptosis and autophagy regulator 1) Expression of this gene is induced by estrogen and the encoded protein has been characterized as a transmembrane protein. The encoded protein has been found in to correlate with survival in certain carcinomas (PMID: 21102415) and may be important for cellular response to stress (PMID: 21072319). Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELAPOR1	NM_020775.5	c.153+22355T>C		intron_variant	Intron 1 of 21	ENST00000369939.8	NP_065826.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELAPOR1	ENST00000369939.8	c.153+22355T>C		intron_variant	Intron 1 of 21	5	NM_020775.5	ENSP00000358955.3

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88286 AN: 151944 Hom.: 27610 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.581 AC: 88330 AN: 152062 Hom.: 27616 Cov.: 32 AF XY: 0.586 AC XY: 43536 AN XY: 74328

African (AFR) AF: 0.344 AC: 14256 AN: 41438

American (AMR) AF: 0.628 AC: 9595 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2084 AN: 3472

East Asian (EAS) AF: 0.917 AC: 4748 AN: 5180

South Asian (SAS) AF: 0.626 AC: 3020 AN: 4822

European-Finnish (FIN) AF: 0.691 AC: 7299 AN: 10566

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45235 AN: 67980

Other (OTH) AF: 0.580 AC: 1226 AN: 2112

Alfa AF: 0.619 Hom.: 10791

Bravo AF: 0.568

Asia WGS AF: 0.723 AC: 2511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.4
DANN	Benign	0.69
PhyloP100		1.9
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: rs591209; hg19: chr1-109679313;