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

Variant summary

Our verdict is Benign. Variant got -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

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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

GnomAD3 exomes

AF:

0.784

AC:

197031

AN:

251342

Hom.:

79374

AF XY:

0.789

AC XY:

107206

AN XY:

135842

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 SAS exome

AF:

0.872

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

Gnomad4 AFR exome

AF:

0.352

Gnomad4 AMR exome

AF:

0.843

Gnomad4 ASJ exome

AF:

0.710

Gnomad4 EAS exome

AF:

0.979

Gnomad4 SAS exome

AF:

0.868

Gnomad4 FIN exome

AF:

0.839

Gnomad4 NFE exome

AF:

0.766

Gnomad4 OTH exome

AF:

0.749

GnomAD4 genome

AF:

0.669

AC:

101824

AN:

152160

Hom.:

36892

Cov.:

AF XY:

0.678

AC XY:

50446

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.370

Gnomad4 AMR

AF:

0.753

Gnomad4 ASJ

AF:

0.699

Gnomad4 EAS

AF:

0.972

Gnomad4 SAS

AF:

0.877

Gnomad4 FIN

AF:

0.840

Gnomad4 NFE

AF:

0.766

Gnomad4 OTH

AF:

0.669

Alfa

AF:

0.733

Hom.:

54567

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

DANN

Benign

0.68

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over