dbSNP rs10494104: ELAPOR1:c.153+23543G>A (chr1-109137879-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.21

Publications

1 publications found

Variant links:

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]

ELAPOR1 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_020775.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

Gene	Transcript	Tags	HGVSc	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

Gene	Transcript	Tags	HGVSc	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.:

show subpopulations

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.:

AF XY:

0.107

AC XY:

7949

AN XY:

74436

show subpopulations

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:

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.0613

AC:

4167

AN:

68010

Other (OTH)

AF:

0.0995

AC:

210

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

736

1472

2208

2944

3680

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

352

528

704

880

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.74

PhyloP100

-1.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over