chr1-213996654-C-T
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001270616.2(PROX1):c.119C>T(p.Thr40Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,892 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T40R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001270616.2 missense
Scores
Clinical Significance
Conservation
Publications
Genome browser will be placed here
ACMG classification
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PROX1 | ENST00000366958.9 | c.119C>T | p.Thr40Met | missense_variant | Exon 2 of 5 | 1 | NM_001270616.2 | ENSP00000355925.4 | ||
PROX1 | ENST00000435016.2 | c.119C>T | p.Thr40Met | missense_variant | Exon 2 of 5 | 1 | ENSP00000400694.1 | |||
PROX1 | ENST00000471129.1 | c.119C>T | p.Thr40Met | missense_variant | Exon 2 of 2 | 3 | ENSP00000419517.1 | |||
PROX1 | ENST00000607425.1 | c.119C>T | p.Thr40Met | missense_variant | Exon 2 of 2 | 3 | ENSP00000475357.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727246 show subpopulations
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at