3-193489591-T-A

Variant names:

• chr3-193489591-T-A
• rs6444724
• NM_032279.4:c.738+139A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 18 publications found

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]

ACMG classification

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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032279.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP13A4	NM_032279.4	MANE Select	c.738+139A>T		intron	N/A	NP_115655.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP13A4	ENST00000342695.9	TSL:1 MANE Select	c.738+139A>T		intron	N/A	ENSP00000339182.4
	ATP13A4	ENST00000490925.5	TSL:1	n.846+139A>T		intron	N/A
	ATP13A4	ENST00000392443.7	TSL:5	c.738+139A>T		intron	N/A	ENSP00000376238.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 683672 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 362450

African (AFR) AF: 0.00 AC: 0 AN: 17382

American (AMR) AF: 0.00 AC: 0 AN: 32534

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16916

East Asian (EAS) AF: 0.00 AC: 0 AN: 34798

South Asian (SAS) AF: 0.00 AC: 0 AN: 59100

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 41410

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2408

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 445774

Other (OTH) AF: 0.00 AC: 0 AN: 33350

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 10662

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.9
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

Other links and lift over

dbSNP: rs6444724; hg19: chr3-193207380;