chrX-154460355-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_017514.5(PLXNA3):c.172C>T(p.Pro58Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0011 in 1,209,562 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 409 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_017514.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXNA3 | NM_017514.5 | c.172C>T | p.Pro58Ser | missense_variant | 2/33 | ENST00000369682.4 | |
PLXNA3 | XM_047442247.1 | c.172C>T | p.Pro58Ser | missense_variant | 2/22 | ||
PLXNA3 | XR_007068193.1 | n.347C>T | non_coding_transcript_exon_variant | 2/32 | |||
PLXNA3 | XR_430556.4 | n.347C>T | non_coding_transcript_exon_variant | 2/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXNA3 | ENST00000369682.4 | c.172C>T | p.Pro58Ser | missense_variant | 2/33 | 1 | NM_017514.5 | P1 | |
PLXNA3 | ENST00000495040.1 | n.146-744C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000959 AC: 108AN: 112571Hom.: 0 Cov.: 25 AF XY: 0.000778 AC XY: 27AN XY: 34715
GnomAD3 exomes AF: 0.000798 AC: 143AN: 179184Hom.: 0 AF XY: 0.000613 AC XY: 40AN XY: 65256
GnomAD4 exome AF: 0.00112 AC: 1224AN: 1096938Hom.: 0 Cov.: 31 AF XY: 0.00105 AC XY: 382AN XY: 362712
GnomAD4 genome AF: 0.000959 AC: 108AN: 112624Hom.: 0 Cov.: 25 AF XY: 0.000776 AC XY: 27AN XY: 34778
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 28, 2022 | The c.172C>T (p.P58S) alteration is located in exon 2 (coding exon 1) of the PLXNA3 gene. This alteration results from a C to T substitution at nucleotide position 172, causing the proline (P) at amino acid position 58 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
PLXNA3-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 30, 2021 | 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). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at