rs17034458

Variant names:

• chr1-109201646-G-T
• rs17034458
• NM_020775.5:c.2973+746G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020775.5(ELAPOR1):​c.2973+746G>T variant causes a intron change. The variant allele was found at a frequency of 0.085 in 152,216 control chromosomes in the GnomAD database, including 661 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 0.085 (661 hom., cov: 32)
• Consequence: ELAPOR1 NM_020775.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.78
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELAPOR1	NM_020775.5	MANE Select	c.2973+746G>T		intron	N/A	NP_065826.3
	ELAPOR1	NM_001267048.2		c.2712+746G>T		intron	N/A	NP_001253977.2
	ELAPOR1	NM_001284352.2		c.2667+746G>T		intron	N/A	NP_001271281.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELAPOR1	ENST00000369939.8	TSL:5 MANE Select	c.2973+746G>T		intron	N/A	ENSP00000358955.3
	ELAPOR1	ENST00000529753.5	TSL:1	c.2712+746G>T		intron	N/A	ENSP00000434595.1
	ELAPOR1	ENST00000369936.2	TSL:1	n.2130+746G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0850 AC: 12933 AN: 152098 Hom.: 660 Cov.: 32

Gnomad AFR AF: 0.0486

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.0859

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0834

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.0850 AC: 12943 AN: 152216 Hom.: 661 Cov.: 32 AF XY: 0.0846 AC XY: 6299 AN XY: 74420

African (AFR) AF: 0.0488 AC: 2029 AN: 41538

American (AMR) AF: 0.0858 AC: 1311 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 501 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5186

South Asian (SAS) AF: 0.0833 AC: 401 AN: 4816

European-Finnish (FIN) AF: 0.100 AC: 1063 AN: 10602

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.106 AC: 7200 AN: 68000

Other (OTH) AF: 0.114 AC: 242 AN: 2114

Alfa AF: 0.0790 Hom.: 239

Bravo AF: 0.0831

Asia WGS AF: 0.0430 AC: 150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.4
DANN	Benign	0.52
PhyloP100		3.8
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: rs17034458; hg19: chr1-109744268;