chrX-154460397-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_017514.5(PLXNA3):c.214G>A(p.Glu72Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000746 in 1,205,870 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_017514.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXNA3 | NM_017514.5 | c.214G>A | p.Glu72Lys | missense_variant | 2/33 | ENST00000369682.4 | |
PLXNA3 | XM_047442247.1 | c.214G>A | p.Glu72Lys | missense_variant | 2/22 | ||
PLXNA3 | XR_007068193.1 | n.389G>A | non_coding_transcript_exon_variant | 2/32 | |||
PLXNA3 | XR_430556.4 | n.389G>A | non_coding_transcript_exon_variant | 2/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXNA3 | ENST00000369682.4 | c.214G>A | p.Glu72Lys | missense_variant | 2/33 | 1 | NM_017514.5 | P1 | |
PLXNA3 | ENST00000495040.1 | n.146-702G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000177 AC: 2AN: 112840Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 34996
GnomAD3 exomes AF: 0.0000116 AC: 2AN: 172841Hom.: 0 AF XY: 0.0000166 AC XY: 1AN XY: 60175
GnomAD4 exome AF: 0.00000640 AC: 7AN: 1093030Hom.: 0 Cov.: 31 AF XY: 0.00000278 AC XY: 1AN XY: 359330
GnomAD4 genome ? AF: 0.0000177 AC: 2AN: 112840Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 34996
ClinVar
Submissions by phenotype
Autism;C0152423:Microtia Uncertain:1
Uncertain significance, no assertion criteria provided | research | Division of Human Genetics, Children's Hospital of Philadelphia | Aug 22, 2016 | Observed autism and left ear microtia with hearing loss - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at