rs10494104

chr1-109137879-G-A

Variant summary

Our verdict is Benign. Variant got -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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ELAPOR1	NM_020775.5	c.153+23543G>A		intron_variant		ENST00000369939.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELAPOR1	ENST00000369939.8	c.153+23543G>A		intron_variant		5	NM_020775.5	P1

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

Gnomad4 AMR AF: 0.0573

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0836

Gnomad4 FIN AF: 0.0867

Gnomad4 NFE AF: 0.0613

Gnomad4 OTH AF: 0.0995

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

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;