rs10494103

Variant names:

• chr1-109131659-T-C
• rs10494103
• NM_020775.5:c.153+17323T>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+17323T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,160 control chromosomes in the GnomAD database, including 1,292 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 0.11 (1292 hom., cov: 32)
• Consequence: ELAPOR1 NM_020775.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELAPOR1	NM_020775.5	c.153+17323T>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+17323T>C		intron_variant	Intron 1 of 21	5	NM_020775.5	ENSP00000358955.3

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16383 AN: 152042 Hom.: 1285 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0575

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0843

Gnomad FIN AF: 0.0866

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0612

Gnomad OTH AF: 0.0992

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

GnomAD4 genome AF: 0.108 AC: 16426 AN: 152160 Hom.: 1292 Cov.: 32 AF XY: 0.107 AC XY: 7943 AN XY: 74400

African (AFR) AF: 0.224 AC: 9274 AN: 41472

American (AMR) AF: 0.0573 AC: 876 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 462 AN: 3472

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5192

South Asian (SAS) AF: 0.0839 AC: 405 AN: 4826

European-Finnish (FIN) AF: 0.0866 AC: 917 AN: 10590

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0612 AC: 4160 AN: 68014

Other (OTH) AF: 0.0982 AC: 207 AN: 2108

Alfa AF: 0.0805 Hom.: 1816

Bravo AF: 0.110

Asia WGS AF: 0.0410 AC: 142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.59
PhyloP100		1.6
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: rs10494103; hg19: chr1-109674281;