chr10-20245416-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032812.9(PLXDC2):c.1384A>T(p.Ile462Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,613,898 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032812.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXDC2 | NM_032812.9 | c.1384A>T | p.Ile462Phe | missense_variant | 13/14 | ENST00000377252.5 | |
PLXDC2 | NM_001282736.2 | c.1237A>T | p.Ile413Phe | missense_variant | 12/13 | ||
PLXDC2 | XM_011519750.3 | c.1384A>T | p.Ile462Phe | missense_variant | 13/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXDC2 | ENST00000377252.5 | c.1384A>T | p.Ile462Phe | missense_variant | 13/14 | 1 | NM_032812.9 | P1 | |
PLXDC2 | ENST00000377242.7 | c.1237A>T | p.Ile413Phe | missense_variant | 12/13 | 1 | |||
PLXDC2 | ENST00000377238.2 | n.1159A>T | non_coding_transcript_exon_variant | 12/13 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 251304Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135812
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461700Hom.: 0 Cov.: 34 AF XY: 0.0000330 AC XY: 24AN XY: 727156
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.1384A>T (p.I462F) alteration is located in exon 13 (coding exon 13) of the PLXDC2 gene. This alteration results from a A to T substitution at nucleotide position 1384, causing the isoleucine (I) at amino acid position 462 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at