3-194406320-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001367549.1(ATP13A3):​c.3574-204G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 151,956 control chromosomes in the GnomAD database, including 14,484 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.37 ( 14484 hom., cov: 32)

Consequence

ATP13A3
NM_001367549.1 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.03
Variant links:
Genes affected
ATP13A3 (HGNC:24113): (ATPase 13A3) ATP13A3 is a member of the P-type ATPase family of proteins that transport a variety of cations across membranes. Other P-type ATPases include ATP7B (MIM 606882) and ATP7A (MIM 300011).[supplied by OMIM, Aug 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BP6
Variant 3-194406320-C-T is Benign according to our data. Variant chr3-194406320-C-T is described in ClinVar as [Benign]. Clinvar id is 1252466.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ATP13A3NM_001367549.1 linkc.3574-204G>A intron_variant Intron 33 of 33 ENST00000645319.2 NP_001354478.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ATP13A3ENST00000645319.2 linkc.3574-204G>A intron_variant Intron 33 of 33 NM_001367549.1 ENSP00000494937.2 A0A2R8Y635

Frequencies

GnomAD3 genomes
AF:
0.369
AC:
55967
AN:
151838
Hom.:
14438
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.737
Gnomad AMI
AF:
0.204
Gnomad AMR
AF:
0.269
Gnomad ASJ
AF:
0.270
Gnomad EAS
AF:
0.287
Gnomad SAS
AF:
0.379
Gnomad FIN
AF:
0.218
Gnomad MID
AF:
0.301
Gnomad NFE
AF:
0.204
Gnomad OTH
AF:
0.367
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.369
AC:
56066
AN:
151956
Hom.:
14484
Cov.:
32
AF XY:
0.367
AC XY:
27276
AN XY:
74276
show subpopulations
Gnomad4 AFR
AF:
0.737
Gnomad4 AMR
AF:
0.268
Gnomad4 ASJ
AF:
0.270
Gnomad4 EAS
AF:
0.287
Gnomad4 SAS
AF:
0.379
Gnomad4 FIN
AF:
0.218
Gnomad4 NFE
AF:
0.204
Gnomad4 OTH
AF:
0.366
Alfa
AF:
0.282
Hom.:
1084
Bravo
AF:
0.390
Asia WGS
AF:
0.370
AC:
1288
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
May 10, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.73
DANN
Benign
0.47

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: rs13324377; hg19: chr3-194127049; API