Genetic Variant ENSG00000293063:n.71-13T>A (chr3-193581919-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000449483.1(ENSG00000293063):n.71-13T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,728 control chromosomes in the GnomAD database, including 21,481 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 0.52 ( 21478 hom., cov: 29)

Exomes 𝑓: 1.0 ( 3 hom. )

Consequence

ENSG00000293063
ENST00000449483.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.494

Publications

6 publications found

Variant links:

Genes affected

ENSG00000293063 (HGNC:):

ENSG00000293063 links:

ATP13A4 (HGNC:25422): (ATPase 13A4) Predicted to enable ATPase-coupled cation transmembrane transporter activity. Predicted to be involved in cellular calcium ion homeostasis. Predicted to be located in endoplasmic reticulum membrane and endosome membrane. [provided by Alliance of Genome Resources, Apr 2022]

ATP13A4 links:

Genome browser will be placed here

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=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
ATP13A4	XM_047449063.1 link	c.-165-13T>A	intron_variant	Intron 1 of 31	XP_047305019.1
ATP13A4	XM_017007319.2 link	c.-165-13T>A	intron_variant	Intron 1 of 26	XP_016862808.2
ATP13A4	XR_007095757.1 link	n.100-13T>A	intron_variant	Intron 1 of 25

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293063	ENST00000449483.1 link	n.71-13T>A		intron_variant	Intron 1 of 2	3
ATP13A4	ENST00000489140.1 link	n.92-13T>A		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.523

AC:

79264

AN:

151604

Hom.:

21445

Cov.:

show subpopulations

Gnomad AFR

AF:

0.655

Gnomad AMI

AF:

0.565

Gnomad AMR

AF:

0.453

Gnomad ASJ

AF:

0.488

Gnomad EAS

AF:

0.398

Gnomad SAS

AF:

0.435

Gnomad FIN

AF:

0.573

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.469

Gnomad OTH

AF:

0.492

GnomAD4 exome

AF:

1.00

AC:

AN:

Hom.:

Cov.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

GnomAD4 genome

AF:

0.523

AC:

79349

AN:

151722

Hom.:

21478

Cov.:

AF XY:

0.523

AC XY:

38757

AN XY:

74132

show subpopulations

African (AFR)

AF:

0.655

AC:

27097

AN:

41370

American (AMR)

AF:

0.453

AC:

6899

AN:

15232

Ashkenazi Jewish (ASJ)

AF:

0.488

AC:

1691

AN:

3468

East Asian (EAS)

AF:

0.398

AC:

2052

AN:

5160

South Asian (SAS)

AF:

0.434

AC:

2080

AN:

4798

European-Finnish (FIN)

AF:

0.573

AC:

6009

AN:

10488

Middle Eastern (MID)

AF:

0.425

AC:

125

AN:

294

European-Non Finnish (NFE)

AF:

0.469

AC:

31844

AN:

67898

Other (OTH)

AF:

0.493

AC:

1038

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

1821

3642

5464

7285

9106

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

698

1396

2094

2792

3490

<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:

0.511

Hom.:

2510

Bravo

AF:

0.522

Asia WGS

AF:

0.430

AC:

1497

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

5.4

(source)

DANN

Benign

0.83

PhyloP100

-0.49

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over