Genetic Variant NM_032279.4:c.738+139A>T (chr3-193489591-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_032279.4(ATP13A4):c.738+139A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ATP13A4
NM_032279.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00400

Publications

18 publications found

Variant links:

Genes affected

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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ATP13A4	NM_032279.4 link	c.738+139A>T	intron_variant	Intron 7 of 29	ENST00000342695.9	NP_115655.2	Q4VNC1-1B3KU47
ATP13A4	XM_047449063.1 link	c.867+139A>T	intron_variant	Intron 9 of 31		XP_047305019.1
ATP13A4	XM_017007319.2 link	c.867+139A>T	intron_variant	Intron 9 of 26		XP_016862808.2
ATP13A4	XR_007095757.1 link	n.1131+139A>T	intron_variant	Intron 9 of 25

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP13A4	ENST00000342695.9 link	c.738+139A>T		intron_variant	Intron 7 of 29	1	NM_032279.4	ENSP00000339182.4		Q4VNC1-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

683672

Hom.:

AF XY:

0.00

AC XY:

AN XY:

362450

African (AFR)

AF:

0.00

AC:

AN:

17382

American (AMR)

AF:

0.00

AC:

AN:

32534

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

16916

East Asian (EAS)

AF:

0.00

AC:

AN:

34798

South Asian (SAS)

AF:

0.00

AC:

AN:

59100

European-Finnish (FIN)

AF:

0.00

AC:

AN:

41410

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2408

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

445774

Other (OTH)

AF:

0.00

AC:

AN:

33350

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

10662

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.9

(source)

DANN

Benign

0.58

PhyloP100

-0.0040

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over