10-19817084-C-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_032812.9(PLXDC2):c.5C>A(p.Ala2Glu) variant causes a missense change. The variant allele was found at a frequency of 0.0000232 in 1,549,604 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000024 ( 0 hom. )
Consequence
PLXDC2
NM_032812.9 missense
NM_032812.9 missense
Scores
3
6
9
Clinical Significance
Conservation
PhyloP100: 3.59
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXDC2 | NM_032812.9 | c.5C>A | p.Ala2Glu | missense_variant | 1/14 | ENST00000377252.5 | |
PLXDC2 | NM_001282736.2 | c.5C>A | p.Ala2Glu | missense_variant | 1/13 | ||
PLXDC2 | XM_011519750.3 | c.5C>A | p.Ala2Glu | missense_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXDC2 | ENST00000377252.5 | c.5C>A | p.Ala2Glu | missense_variant | 1/14 | 1 | NM_032812.9 | P1 | |
PLXDC2 | ENST00000377242.7 | c.5C>A | p.Ala2Glu | missense_variant | 1/13 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152008Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000243 AC: 34AN: 1397596Hom.: 0 Cov.: 32 AF XY: 0.0000232 AC XY: 16AN XY: 689782
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 152008Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74228
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.5C>A (p.A2E) alteration is located in exon 1 (coding exon 1) of the PLXDC2 gene. This alteration results from a C to A substitution at nucleotide position 5, causing the alanine (A) at amino acid position 2 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T
M_CAP
Benign
D
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Pathogenic
D;D
Sift4G
Pathogenic
D;D
Polyphen
D;D
Vest4
MutPred
Gain of solvent accessibility (P = 0.0456);Gain of solvent accessibility (P = 0.0456);
MVP
MPC
0.59
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at