rs17034354

Variant names:

• chr1-109200545-A-C
• rs17034354
• NM_020775.5:c.2808-190A>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.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
• Publications: 5 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=-0.78).
• 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 rank	MANE	Protein	UniProt
ELAPOR1	NM_020775.5	c.2808-190A>C		intron_variant	Intron 20 of 21	ENST00000369939.8	NP_065826.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELAPOR1	ENST00000369939.8	c.2808-190A>C		intron_variant	Intron 20 of 21	5	NM_020775.5	ENSP00000358955.3

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

African (AFR) AF: 0.115 AC: 4758 AN: 41540

American (AMR) AF: 0.0916 AC: 1402 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3470

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5188

South Asian (SAS) AF: 0.0860 AC: 415 AN: 4826

European-Finnish (FIN) AF: 0.0914 AC: 970 AN: 10608

Middle Eastern (MID) AF: 0.207 AC: 60 AN: 290

European-Non Finnish (NFE) AF: 0.106 AC: 7192 AN: 68004

Other (OTH) AF: 0.126 AC: 267 AN: 2112

Alfa AF: 0.110 Hom.: 1676

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
PhyloP100		0.37
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: rs17034354; hg19: chr1-109743167;