Genetic Variant ATP6V0E2-AS1:n.242T>G (chr7-149873604-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000461019.5(ATP6V0E2-AS1):n.242T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 268,134 control chromosomes in the GnomAD database, including 54,758 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 0.65 ( 33792 hom., cov: 35)

Exomes 𝑓: 0.59 ( 20966 hom. )

Consequence

ATP6V0E2-AS1
ENST00000461019.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.699

Publications

8 publications found

Variant links:

Genes affected

ATP6V0E2-AS1 (HGNC:44180): (ATP6V0E2 antisense RNA 1)

ATP6V0E2-AS1 links:

ATP6V0E2 (HGNC:21723): (ATPase H+ transporting V0 subunit e2) Multisubunit vacuolar-type proton pumps, or H(+)-ATPases, acidify various intracellular compartments, such as vacuoles, clathrin-coated and synaptic vesicles, endosomes, lysosomes, and chromaffin granules. H(+)-ATPases are also found in plasma membranes of specialized cells, where they play roles in urinary acidification, bone resorption, and sperm maturation. Multiple subunits form H(+)-ATPases, with proteins of the V1 class hydrolyzing ATP for energy to transport H+, and proteins of the V0 class forming an integral membrane domain through which H+ is transported. ATP6V0E2 encodes an isoform of the H(+)-ATPase V0 e subunit, an essential proton pump component (Blake-Palmer et al., 2007 [PubMed 17350184]).[supplied by OMIM, Mar 2008]

ATP6V0E2 links:

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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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
ATP6V0E2-AS1	NR_027040.1 link	n.259T>G	non_coding_transcript_exon_variant	Exon 1 of 4
ATP6V0E2	NR_110612.1 link	n.637A>C	non_coding_transcript_exon_variant	Exon 1 of 5
ATP6V0E2	NM_001367791.1 link	c.-816A>C	5_prime_UTR_variant	Exon 1 of 5	NP_001354720.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
ATP6V0E2-AS1	ENST00000461019.5 link	n.242T>G	non_coding_transcript_exon_variant	Exon 1 of 4	1
ATP6V0E2	ENST00000421974.7 link	c.-462A>C	5_prime_UTR_variant	Exon 1 of 3	1	ENSP00000411672.3	Q8NHE4-2E9PAS2
ATP6V0E2	ENST00000456496.7 link	c.-462A>C	5_prime_UTR_variant	Exon 1 of 4	1	ENSP00000410220.3	Q8NHE4-1

Frequencies

GnomAD3 genomes

AF:

0.655

AC:

99501

AN:

151978

Hom.:

33762

Cov.:

show subpopulations

Gnomad AFR

AF:

0.828

Gnomad AMI

AF:

0.587

Gnomad AMR

AF:

0.572

Gnomad ASJ

AF:

0.565

Gnomad EAS

AF:

0.378

Gnomad SAS

AF:

0.407

Gnomad FIN

AF:

0.544

Gnomad MID

AF:

0.634

Gnomad NFE

AF:

0.629

Gnomad OTH

AF:

0.644

GnomAD4 exome

AF:

0.594

AC:

68885

AN:

116046

Hom.:

20966

Cov.:

AF XY:

0.594

AC XY:

34415

AN XY:

57930

show subpopulations

African (AFR)

AF:

0.828

AC:

3061

AN:

3696

American (AMR)

AF:

0.546

AC:

1697

AN:

3110

Ashkenazi Jewish (ASJ)

AF:

0.570

AC:

2682

AN:

4704

East Asian (EAS)

AF:

0.394

AC:

4232

AN:

10736

South Asian (SAS)

AF:

0.362

AC:

582

AN:

1608

European-Finnish (FIN)

AF:

0.544

AC:

4547

AN:

8354

Middle Eastern (MID)

AF:

0.611

AC:

406

AN:

664

European-Non Finnish (NFE)

AF:

0.623

AC:

46658

AN:

74946

Other (OTH)

AF:

0.610

AC:

5020

AN:

8228

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1293

2585

3878

5170

6463

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

218

436

654

872

1090

<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:

0.655

AC:

99586

AN:

152088

Hom.:

33792

Cov.:

AF XY:

0.644

AC XY:

47890

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.828

AC:

34383

AN:

41528

American (AMR)

AF:

0.572

AC:

8750

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.565

AC:

1961

AN:

3472

East Asian (EAS)

AF:

0.379

AC:

1943

AN:

5132

South Asian (SAS)

AF:

0.405

AC:

1954

AN:

4822

European-Finnish (FIN)

AF:

0.544

AC:

5746

AN:

10568

Middle Eastern (MID)

AF:

0.640

AC:

187

AN:

292

European-Non Finnish (NFE)

AF:

0.629

AC:

42765

AN:

67942

Other (OTH)

AF:

0.644

AC:

1362

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1761

3522

5282

7043

8804

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

776

1552

2328

3104

3880

<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:

0.670

Hom.:

3517

Bravo

AF:

0.669

Asia WGS

AF:

0.426

AC:

1478

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

7.9

(source)

DANN

Benign

0.71

PhyloP100

-0.70

PromoterAI

0.083

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

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