3-129559661-T-G
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_015103.3(PLXND1):āc.5256A>Cā(p.Gly1752=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000595 in 1,612,620 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 Likely benign (ā ).
Frequency
Genomes: š 0.000053 ( 0 hom., cov: 33)
Exomes š: 0.000060 ( 0 hom. )
Consequence
PLXND1
NM_015103.3 synonymous
NM_015103.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.83
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 Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
Variant 3-129559661-T-G is Benign according to our data. Variant chr3-129559661-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 765142.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.83 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXND1 | NM_015103.3 | c.5256A>C | p.Gly1752= | synonymous_variant | 32/36 | ENST00000324093.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXND1 | ENST00000324093.9 | c.5256A>C | p.Gly1752= | synonymous_variant | 32/36 | 1 | NM_015103.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152040Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000720 AC: 18AN: 250058Hom.: 0 AF XY: 0.0000666 AC XY: 9AN XY: 135140
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GnomAD4 exome AF: 0.0000603 AC: 88AN: 1460462Hom.: 0 Cov.: 32 AF XY: 0.0000606 AC XY: 44AN XY: 726516
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GnomAD4 genome AF: 0.0000526 AC: 8AN: 152158Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74384
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 20, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at