Genetic Variant ELAPOR1:p.Asn656Asn (chr1-109194441-C-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_020775.5(ELAPOR1):c.1968C>T(p.Asn656Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 1,611,524 control chromosomes in the GnomAD database, including 476,407 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 ( 36892 hom., cov: 33)

Exomes 𝑓: 0.77 ( 439515 hom. )

Consequence

ELAPOR1
NM_020775.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.19

Publications

23 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 -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BP7

Synonymous conserved (PhyloP=-2.18 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.1968C>T	p.Asn656Asn	synonymous_variant	Exon 15 of 22	ENST00000369939.8	NP_065826.3	Q6UXG2-1B4DWM4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELAPOR1	ENST00000369939.8 link	c.1968C>T	p.Asn656Asn	synonymous_variant	Exon 15 of 22	5	NM_020775.5	ENSP00000358955.3		Q6UXG2-1

Frequencies

GnomAD3 genomes

AF:

0.669

AC:

101776

AN:

152042

Hom.:

36875

Cov.:

show subpopulations

Gnomad AFR

AF:

0.371

Gnomad AMI

AF:

0.701

Gnomad AMR

AF:

0.753

Gnomad ASJ

AF:

0.699

Gnomad EAS

AF:

0.972

Gnomad SAS

AF:

0.877

Gnomad FIN

AF:

0.840

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.766

Gnomad OTH

AF:

0.667

GnomAD2 exomes

AF:

0.784

AC:

197031

AN:

251342

AF XY:

0.789

show subpopulations

Gnomad AFR exome

AF:

0.364

Gnomad AMR exome

AF:

0.853

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:

1125432

AN:

1459364

Hom.:

439515

Cov.:

AF XY:

0.774

AC XY:

562389

AN XY:

726144

show subpopulations

African (AFR)

AF:

0.352

AC:

11771

AN:

33426

American (AMR)

AF:

0.843

AC:

37702

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.710

AC:

18549

AN:

26110

East Asian (EAS)

AF:

0.979

AC:

38861

AN:

39698

South Asian (SAS)

AF:

0.868

AC:

74876

AN:

86216

European-Finnish (FIN)

AF:

0.839

AC:

44749

AN:

53362

Middle Eastern (MID)

AF:

0.659

AC:

3794

AN:

5754

European-Non Finnish (NFE)

AF:

0.766

AC:

849939

AN:

1109766

Other (OTH)

AF:

0.749

AC:

45191

AN:

60312

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.437

Heterozygous variant carriers

13699

27397

41096

54794

68493

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20330

40660

60990

81320

101650

<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:

101824

AN:

152160

Hom.:

36892

Cov.:

AF XY:

0.678

AC XY:

50446

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.370

AC:

15357

AN:

41478

American (AMR)

AF:

0.753

AC:

11519

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.699

AC:

2423

AN:

3468

East Asian (EAS)

AF:

0.972

AC:

5021

AN:

5164

South Asian (SAS)

AF:

0.877

AC:

4240

AN:

4834

European-Finnish (FIN)

AF:

0.840

AC:

8904

AN:

10600

Middle Eastern (MID)

AF:

0.626

AC:

184

AN:

294

European-Non Finnish (NFE)

AF:

0.766

AC:

52125

AN:

68006

Other (OTH)

AF:

0.669

AC:

1413

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1489

2978

4466

5955

7444

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:

0.727

Hom.:

117269

Bravo

AF:

0.650

Asia WGS

AF:

0.880

AC:

3059

AN:

3478

EpiCase

AF:

0.754

EpiControl

AF:

0.747

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

0.24

(source)

DANN

Benign

0.68

PhyloP100

-2.2

Mutation Taster

=95/5

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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