rs10494104

Variant names:

• chr1-109137879-G-A
• rs10494104
• NM_020775.5:c.153+23543G>A

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+23543G>A 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 152,214 control chromosomes in the GnomAD database, including 1,295 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 (1295 hom., cov: 33)
• Consequence: ELAPOR1 NM_020775.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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=-0.95).
• 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+23543G>A		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+23543G>A		intron_variant	Intron 1 of 21	5	NM_020775.5	ENSP00000358955.3

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16412 AN: 152096 Hom.: 1289 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0575

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0840

Gnomad FIN AF: 0.0867

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0613

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.108 AC: 16452 AN: 152214 Hom.: 1295 Cov.: 33 AF XY: 0.107 AC XY: 7949 AN XY: 74436

Gnomad4 AFR AF: 0.224 AC: 0.223805 AN: 0.223805

Gnomad4 AMR AF: 0.0573 AC: 0.0572774 AN: 0.0572774

Gnomad4 ASJ AF: 0.133 AC: 0.133429 AN: 0.133429

Gnomad4 EAS AF: 0.000386 AC: 0.000385654 AN: 0.000385654

Gnomad4 SAS AF: 0.0836 AC: 0.0836093 AN: 0.0836093

Gnomad4 FIN AF: 0.0867 AC: 0.0867107 AN: 0.0867107

Gnomad4 NFE AF: 0.0613 AC: 0.0612704 AN: 0.0612704

Gnomad4 OTH AF: 0.0995 AC: 0.0995261 AN: 0.0995261

Alfa AF: 0.0886 Hom.: 112

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	-0.95
CADD	Benign	0.58
DANN	Benign	0.74
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

Publications

LitVar

Other links and lift over

dbSNP: rs10494104; hg19: chr1-109680501;