chr10-20001906-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_032812.9(PLXDC2):c.244G>A(p.Val82Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000437 in 1,613,610 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_032812.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXDC2 | NM_032812.9 | c.244G>A | p.Val82Ile | missense_variant | 2/14 | ENST00000377252.5 | |
PLXDC2 | NM_001282736.2 | c.244G>A | p.Val82Ile | missense_variant | 2/13 | ||
PLXDC2 | XM_011519750.3 | c.244G>A | p.Val82Ile | missense_variant | 2/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXDC2 | ENST00000377252.5 | c.244G>A | p.Val82Ile | missense_variant | 2/14 | 1 | NM_032812.9 | P1 | |
PLXDC2 | ENST00000377242.7 | c.244G>A | p.Val82Ile | missense_variant | 2/13 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00225 AC: 342AN: 152130Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000582 AC: 146AN: 250844Hom.: 0 AF XY: 0.000465 AC XY: 63AN XY: 135570
GnomAD4 exome AF: 0.000248 AC: 362AN: 1461362Hom.: 2 Cov.: 31 AF XY: 0.000212 AC XY: 154AN XY: 726968
GnomAD4 genome ? AF: 0.00225 AC: 343AN: 152248Hom.: 1 Cov.: 32 AF XY: 0.00219 AC XY: 163AN XY: 74420
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 14, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at