chrX-154460238-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_017514.5(PLXNA3):c.55G>A(p.Gly19Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000146 in 1,208,510 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 50 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G19D) has been classified as Likely benign.
Frequency
Consequence
NM_017514.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXNA3 | NM_017514.5 | c.55G>A | p.Gly19Ser | missense_variant | 2/33 | ENST00000369682.4 | |
PLXNA3 | XM_047442247.1 | c.55G>A | p.Gly19Ser | missense_variant | 2/22 | ||
PLXNA3 | XR_007068193.1 | n.230G>A | non_coding_transcript_exon_variant | 2/32 | |||
PLXNA3 | XR_430556.4 | n.230G>A | non_coding_transcript_exon_variant | 2/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXNA3 | ENST00000369682.4 | c.55G>A | p.Gly19Ser | missense_variant | 2/33 | 1 | NM_017514.5 | P1 | |
PLXNA3 | ENST00000495040.1 | n.146-861G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000801 AC: 9AN: 112420Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 34586
GnomAD3 exomes AF: 0.0000778 AC: 14AN: 179866Hom.: 0 AF XY: 0.0000152 AC XY: 1AN XY: 65880
GnomAD4 exome AF: 0.000153 AC: 168AN: 1096036Hom.: 0 Cov.: 31 AF XY: 0.000138 AC XY: 50AN XY: 362078
GnomAD4 genome ? AF: 0.0000800 AC: 9AN: 112474Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 34650
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2022 | The c.55G>A (p.G19S) alteration is located in exon 2 (coding exon 1) of the PLXNA3 gene. This alteration results from a G to A substitution at nucleotide position 55, causing the glycine (G) at amino acid position 19 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
PLXNA3-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 01, 2023 | The PLXNA3 c.55G>A variant is predicted to result in the amino acid substitution p.Gly19Ser. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.015% of alleles in individuals of European (Non-Finnish) descent in gnomAD, including one hemizygote (http://gnomad.broadinstitute.org/variant/X-153688578-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at