rs17034354

chr1-109200545-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020775.5(ELAPOR1):c.2808-190A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,254 control chromosomes in the GnomAD database, including 881 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 0.10 (881 hom., cov: 32)
• Consequence: ELAPOR1 NM_020775.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371

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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELAPOR1	NM_020775.5	c.2808-190A>C		intron_variant		ENST00000369939.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELAPOR1	ENST00000369939.8	c.2808-190A>C		intron_variant		5	NM_020775.5	P1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15691 AN: 152136 Hom.: 880 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0918

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0859

Gnomad FIN AF: 0.0914

Gnomad MID AF: 0.202

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.103 AC: 15698 AN: 152254 Hom.: 881 Cov.: 32 AF XY: 0.102 AC XY: 7593 AN XY: 74458

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0916

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0860

Gnomad4 FIN AF: 0.0914

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.126

Alfa AF: 0.110 Hom.: 1341

Bravo AF: 0.105

Asia WGS AF: 0.0450 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	11
Dann	Benign	0.80

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: rs17034354; hg19: chr1-109743167;