dbSNP rs2359245: ELAPOR1:p.Pro665Pro (chr1-109194468-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_020775.5(ELAPOR1):c.1995G>A(p.Pro665Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 1,611,922 control chromosomes in the GnomAD database, including 476,261 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 0.67 ( 36875 hom., cov: 33)

Exomes 𝑓: 0.77 ( 439386 hom. )

Consequence

ELAPOR1
NM_020775.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.29

Publications

22 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

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP7

Synonymous conserved (PhyloP=-1.29 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELAPOR1	NM_020775.5 link	c.1995G>A	p.Pro665Pro	synonymous_variant	Exon 15 of 22	ENST00000369939.8	NP_065826.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELAPOR1	ENST00000369939.8 link	c.1995G>A	p.Pro665Pro	synonymous_variant	Exon 15 of 22	5	NM_020775.5	ENSP00000358955.3

Frequencies

GnomAD3 genomes

AF:

0.670

AC:

101773

AN:

151986

Hom.:

36857

Cov.:

show subpopulations

Gnomad AFR

AF:

0.372

Gnomad AMI

AF:

0.702

Gnomad AMR

AF:

0.752

Gnomad ASJ

AF:

0.699

Gnomad EAS

AF:

0.972

Gnomad SAS

AF:

0.876

Gnomad FIN

AF:

0.840

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.766

Gnomad OTH

AF:

0.665

GnomAD2 exomes

AF:

0.784

AC:

197052

AN:

251430

AF XY:

0.789

show subpopulations

Gnomad AFR exome

AF:

0.364

Gnomad AMR exome

AF:

0.852

Gnomad ASJ exome

AF:

0.705

Gnomad EAS exome

AF:

0.971

Gnomad FIN exome

AF:

0.840

Gnomad NFE exome

AF:

0.766

Gnomad OTH exome

AF:

0.773

GnomAD4 exome

AF:

0.771

AC:

1125475

AN:

1459818

Hom.:

439386

Cov.:

AF XY:

0.774

AC XY:

562418

AN XY:

726378

show subpopulations

African (AFR)

AF:

0.349

AC:

11681

AN:

33428

American (AMR)

AF:

0.843

AC:

37690

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.710

AC:

18553

AN:

26120

East Asian (EAS)

AF:

0.979

AC:

38861

AN:

39700

South Asian (SAS)

AF:

0.868

AC:

74854

AN:

86228

European-Finnish (FIN)

AF:

0.839

AC:

44780

AN:

53404

Middle Eastern (MID)

AF:

0.659

AC:

3800

AN:

5762

European-Non Finnish (NFE)

AF:

0.766

AC:

850088

AN:

1110138

Other (OTH)

AF:

0.749

AC:

45168

AN:

60320

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.437

Heterozygous variant carriers

14042

28085

42127

56170

70212

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20338

40676

61014

81352

101690

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.669

AC:

101822

AN:

152104

Hom.:

36875

Cov.:

AF XY:

0.679

AC XY:

50454

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.371

AC:

15383

AN:

41446

American (AMR)

AF:

0.753

AC:

11505

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.699

AC:

2424

AN:

3466

East Asian (EAS)

AF:

0.972

AC:

5015

AN:

5158

South Asian (SAS)

AF:

0.877

AC:

4235

AN:

4830

European-Finnish (FIN)

AF:

0.840

AC:

8898

AN:

10588

Middle Eastern (MID)

AF:

0.626

AC:

184

AN:

294

European-Non Finnish (NFE)

AF:

0.766

AC:

52125

AN:

68016

Other (OTH)

AF:

0.668

AC:

1413

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1492

2984

4476

5968

7460

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

802

1604

2406

3208

4010

<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:

0.729

Hom.:

115305

Bravo

AF:

0.650

Asia WGS

AF:

0.880

AC:

3059

AN:

3478

EpiCase

AF:

0.753

EpiControl

AF:

0.747

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

0.038

(source)

DANN

Benign

0.62

PhyloP100

-1.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over