GeneBe

rs41289971

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7

The NM_033305.3(VPS13A):​c.5979C>A​(p.Arg1993Arg) variant causes a synonymous 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. Synonymous variant affecting the same amino acid position (i.e. R1993R) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

VPS13A
NM_033305.3 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.339

Publications

0 publications found
Variant links:
Genes affected
VPS13A (HGNC:1908): (vacuolar protein sorting 13 homolog A) The protein encoded by this gene may control steps in the cycling of proteins through the trans-Golgi network to endosomes, lysosomes and the plasma membrane. Mutations in this gene cause the autosomal recessive disorder, chorea-acanthocytosis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]
VPS13A Gene-Disease associations (from GenCC):
  • chorea-acanthocytosis
    Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Ambry Genetics

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (REVEL=0.039).
BP7
Synonymous conserved (PhyloP=0.339 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033305.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
VPS13A
NM_033305.3
MANE Select
c.5979C>Ap.Arg1993Arg
synonymous
Exon 45 of 72NP_150648.2Q96RL7-1
VPS13A
NM_001018037.2
c.5862C>Ap.Arg1954Arg
synonymous
Exon 44 of 71NP_001018047.1Q96RL7-3
VPS13A
NM_015186.4
c.5979C>Ap.Arg1993Arg
synonymous
Exon 45 of 69NP_056001.1Q96RL7-2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
VPS13A
ENST00000360280.8
TSL:1 MANE Select
c.5979C>Ap.Arg1993Arg
synonymous
Exon 45 of 72ENSP00000353422.3Q96RL7-1
VPS13A
ENST00000376636.7
TSL:1
c.5862C>Ap.Arg1954Arg
synonymous
Exon 44 of 71ENSP00000365823.3Q96RL7-3
VPS13A
ENST00000419472.1
TSL:1
c.735C>Ap.Arg245Arg
synonymous
Exon 5 of 7ENSP00000414410.1H0Y7P8

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1460974
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
726818
African (AFR)
AF:
0.00
AC:
0
AN:
33430
American (AMR)
AF:
0.00
AC:
0
AN:
44686
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26106
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39628
South Asian (SAS)
AF:
0.00
AC:
0
AN:
86246
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53394
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5756
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1111384
Other (OTH)
AF:
0.00
AC:
0
AN:
60344
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
4
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.28
CADD
Benign
6.3
DANN
Benign
0.61
PhyloP100
0.34
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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

Other links and lift over

dbSNP: rs41289971; hg19: chr9-79938131; API