chr3-129556363-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_015103.3(PLXND1):c.5727G>A(p.Gln1909=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,613,730 control chromosomes in the GnomAD database, including 20,341 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.19 ( 3157 hom., cov: 33)
Exomes 𝑓: 0.15 ( 17184 hom. )
Consequence
PLXND1
NM_015103.3 synonymous
NM_015103.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.650
Genes affected
PLXND1 (HGNC:9107): (plexin D1) Enables protein domain specific binding activity. Predicted to be involved in several processes, including endothelial cell migration; nervous system development; and regulation of angiogenesis. Predicted to act upstream of or within several processes, including circulatory system development; dichotomous subdivision of terminal units involved in salivary gland branching; and positive regulation of protein binding activity. Located in lamellipodium. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
?
Variant 3-129556363-C-T is Benign according to our data. Variant chr3-129556363-C-T is described in ClinVar as [Benign]. Clinvar id is 3059889.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.65 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXND1 | NM_015103.3 | c.5727G>A | p.Gln1909= | synonymous_variant | 36/36 | ENST00000324093.9 | |
PLXND1 | XM_011512589.2 | c.5337G>A | p.Gln1779= | synonymous_variant | 33/33 | ||
PLXND1 | XM_011512592.1 | c.2895G>A | p.Gln965= | synonymous_variant | 24/24 | ||
PLXND1 | XM_011512588.3 | c.*84G>A | 3_prime_UTR_variant | 36/36 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXND1 | ENST00000324093.9 | c.5727G>A | p.Gln1909= | synonymous_variant | 36/36 | 1 | NM_015103.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.187 AC: 28432AN: 152118Hom.: 3140 Cov.: 33
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GnomAD3 exomes AF: 0.168 AC: 42319AN: 251442Hom.: 4131 AF XY: 0.167 AC XY: 22681AN XY: 135892
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GnomAD4 exome AF: 0.146 AC: 212675AN: 1461494Hom.: 17184 Cov.: 32 AF XY: 0.148 AC XY: 107617AN XY: 727066
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GnomAD4 genome ? AF: 0.187 AC: 28485AN: 152236Hom.: 3157 Cov.: 33 AF XY: 0.190 AC XY: 14118AN XY: 74440
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PLXND1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 06, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
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