chr10-20046930-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032812.9(PLXDC2):c.386G>A(p.Arg129Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000285 in 1,612,326 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000027 ( 0 hom. )
Consequence
PLXDC2
NM_032812.9 missense
NM_032812.9 missense
Scores
1
5
13
Clinical Significance
Conservation
PhyloP100: 5.25
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0883117).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXDC2 | NM_032812.9 | c.386G>A | p.Arg129Gln | missense_variant | 3/14 | ENST00000377252.5 | |
PLXDC2 | XM_011519750.3 | c.386G>A | p.Arg129Gln | missense_variant | 3/14 | ||
PLXDC2 | NM_001282736.2 | c.325-21240G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXDC2 | ENST00000377252.5 | c.386G>A | p.Arg129Gln | missense_variant | 3/14 | 1 | NM_032812.9 | P1 | |
PLXDC2 | ENST00000377242.7 | c.325-21240G>A | intron_variant | 1 | |||||
PLXDC2 | ENST00000377238.2 | n.161G>A | non_coding_transcript_exon_variant | 2/13 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 151878Hom.: 0 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0000519 AC: 13AN: 250450Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135426
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GnomAD4 exome AF: 0.0000274 AC: 40AN: 1460328Hom.: 0 Cov.: 30 AF XY: 0.0000234 AC XY: 17AN XY: 726556
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GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 151998Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74268
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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 | Sep 14, 2023 | The c.386G>A (p.R129Q) alteration is located in exon 3 (coding exon 3) of the PLXDC2 gene. This alteration results from a G to A substitution at nucleotide position 386, causing the arginine (R) at amino acid position 129 to be replaced by a glutamine (Q). 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
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Pathogenic
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Benign
T
Sift4G
Benign
T
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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Calibrated prediction
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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