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
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020775.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELAPOR1	NM_020775.5	MANE Select	c.153+23543G>A		intron	N/A	NP_065826.3
	ELAPOR1	NM_001267048.2		c.153+23543G>A		intron	N/A	NP_001253977.2	Q6UXG2-3
	ELAPOR1	NM_001284352.2		c.-33+23543G>A		intron	N/A	NP_001271281.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELAPOR1	ENST00000369939.8	TSL:5 MANE Select	c.153+23543G>A		intron	N/A	ENSP00000358955.3	Q6UXG2-1
	ELAPOR1	ENST00000529753.5	TSL:1	c.153+23543G>A		intron	N/A	ENSP00000434595.1	Q6UXG2-3
	ELAPOR1	ENST00000899218.1		c.153+23543G>A		intron	N/A	ENSP00000569277.1

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

African (AFR) AF: 0.224 AC: 9287 AN: 41496

American (AMR) AF: 0.0573 AC: 876 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 463 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5186

South Asian (SAS) AF: 0.0836 AC: 404 AN: 4832

European-Finnish (FIN) AF: 0.0867 AC: 920 AN: 10610

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

European-Non Finnish (NFE) AF: 0.0613 AC: 4167 AN: 68010

Other (OTH) AF: 0.0995 AC: 210 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.58
DANN	Benign	0.74
PhyloP100		-1.2
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: rs10494104; hg19: chr1-109680501;