rs7630292

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032279.4(ATP13A4):​c.2843-3937C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 149,464 control chromosomes in the GnomAD database, including 4,533 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 0.17 ( 4533 hom., cov: 30)

Consequence

ATP13A4
NM_032279.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.94
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ATP13A4NM_032279.4 linkuse as main transcriptc.2843-3937C>T intron_variant ENST00000342695.9
ATP13A4XM_047449063.1 linkuse as main transcriptc.2972-3937C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ATP13A4ENST00000342695.9 linkuse as main transcriptc.2843-3937C>T intron_variant 1 NM_032279.4 P1Q4VNC1-1

Frequencies

GnomAD3 genomes
AF:
0.173
AC:
25861
AN:
149352
Hom.:
4522
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.377
Gnomad AMI
AF:
0.0958
Gnomad AMR
AF:
0.148
Gnomad ASJ
AF:
0.0805
Gnomad EAS
AF:
0.265
Gnomad SAS
AF:
0.179
Gnomad FIN
AF:
0.0698
Gnomad MID
AF:
0.111
Gnomad NFE
AF:
0.0731
Gnomad OTH
AF:
0.140
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.173
AC:
25913
AN:
149464
Hom.:
4533
Cov.:
30
AF XY:
0.174
AC XY:
12689
AN XY:
72928
show subpopulations
Gnomad4 AFR
AF:
0.377
Gnomad4 AMR
AF:
0.148
Gnomad4 ASJ
AF:
0.0805
Gnomad4 EAS
AF:
0.265
Gnomad4 SAS
AF:
0.179
Gnomad4 FIN
AF:
0.0698
Gnomad4 NFE
AF:
0.0731
Gnomad4 OTH
AF:
0.140
Alfa
AF:
0.0915
Hom.:
1100
Asia WGS
AF:
0.224
AC:
761
AN:
3396

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
1.6
DANN
Benign
0.41

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

LitVar

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

Other links and lift over

dbSNP: rs7630292; hg19: chr3-193136476; API