10-20001883-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_032812.9(PLXDC2):c.221C>T(p.Ala74Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000807 in 1,613,900 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0043 ( 5 hom., cov: 32)
Exomes 𝑓: 0.00044 ( 3 hom. )
Consequence
PLXDC2
NM_032812.9 missense
NM_032812.9 missense
Scores
3
14
Clinical Significance
Conservation
PhyloP100: 1.97
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0041987896).
BP6
?
Variant 10-20001883-C-T is Benign according to our data. Variant chr10-20001883-C-T is described in ClinVar as [Benign]. Clinvar id is 712486.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXDC2 | NM_032812.9 | c.221C>T | p.Ala74Val | missense_variant | 2/14 | ENST00000377252.5 | |
PLXDC2 | NM_001282736.2 | c.221C>T | p.Ala74Val | missense_variant | 2/13 | ||
PLXDC2 | XM_011519750.3 | c.221C>T | p.Ala74Val | missense_variant | 2/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXDC2 | ENST00000377252.5 | c.221C>T | p.Ala74Val | missense_variant | 2/14 | 1 | NM_032812.9 | P1 | |
PLXDC2 | ENST00000377242.7 | c.221C>T | p.Ala74Val | missense_variant | 2/13 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00431 AC: 655AN: 152116Hom.: 5 Cov.: 32
GnomAD3 genomes
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152116
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32
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GnomAD3 exomes AF: 0.00119 AC: 298AN: 250868Hom.: 1 AF XY: 0.000863 AC XY: 117AN XY: 135582
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GnomAD4 exome AF: 0.000441 AC: 645AN: 1461666Hom.: 3 Cov.: 31 AF XY: 0.000382 AC XY: 278AN XY: 727114
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GnomAD4 genome ? AF: 0.00432 AC: 657AN: 152234Hom.: 5 Cov.: 32 AF XY: 0.00406 AC XY: 302AN XY: 74432
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ESP6500AA
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ExAC
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174
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 08, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N
MutationTaster
Benign
D;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Uncertain
D;T
Sift4G
Benign
T;T
Polyphen
P;B
Vest4
MVP
MPC
0.11
ClinPred
T
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