14-74863267-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001243007.2(PROX2):c.568G>A(p.Gly190Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000044 in 1,613,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001243007.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PROX2 | NM_001243007.2 | c.568G>A | p.Gly190Ser | missense_variant | 3/6 | ENST00000556489.4 | NP_001229936.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PROX2 | ENST00000556489.4 | c.568G>A | p.Gly190Ser | missense_variant | 3/6 | 1 | NM_001243007.2 | ENSP00000451223.2 | ||
PROX2 | ENST00000673765.1 | c.568G>A | p.Gly190Ser | missense_variant | 3/5 | ENSP00000501015.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000766 AC: 19AN: 248132Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 134784
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1461512Hom.: 0 Cov.: 32 AF XY: 0.0000660 AC XY: 48AN XY: 727022
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152344Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74500
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 09, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at