chr3-129556632-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_015103.3(PLXND1):c.5646G>A(p.Lys1882=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000102 in 1,612,990 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00071 ( 2 hom., cov: 33)
Exomes 𝑓: 0.000039 ( 0 hom. )
Consequence
PLXND1
NM_015103.3 synonymous
NM_015103.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.17
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.21).
BP6
?
Variant 3-129556632-C-T is Benign according to our data. Variant chr3-129556632-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3050325.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.17 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXND1 | NM_015103.3 | c.5646G>A | p.Lys1882= | synonymous_variant | 35/36 | ENST00000324093.9 | |
PLXND1 | XM_011512588.3 | c.5646G>A | p.Lys1882= | synonymous_variant | 35/36 | ||
PLXND1 | XM_011512589.2 | c.5256G>A | p.Lys1752= | synonymous_variant | 32/33 | ||
PLXND1 | XM_011512592.1 | c.2814G>A | p.Lys938= | synonymous_variant | 23/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXND1 | ENST00000324093.9 | c.5646G>A | p.Lys1882= | synonymous_variant | 35/36 | 1 | NM_015103.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000709 AC: 108AN: 152246Hom.: 2 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
108
AN:
152246
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000160 AC: 40AN: 249470Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 134914
GnomAD3 exomes
AF:
AC:
40
AN:
249470
Hom.:
AF XY:
AC XY:
14
AN XY:
134914
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000390 AC: 57AN: 1460626Hom.: 0 Cov.: 30 AF XY: 0.0000262 AC XY: 19AN XY: 726570
GnomAD4 exome
AF:
AC:
57
AN:
1460626
Hom.:
Cov.:
30
AF XY:
AC XY:
19
AN XY:
726570
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000709 AC: 108AN: 152364Hom.: 2 Cov.: 33 AF XY: 0.000617 AC XY: 46AN XY: 74510
GnomAD4 genome
?
AF:
AC:
108
AN:
152364
Hom.:
Cov.:
33
AF XY:
AC XY:
46
AN XY:
74510
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PLXND1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 15, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at