17-50279259-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153229.3(TMEM92):c.431C>T(p.Pro144Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,736 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P144S) has been classified as Uncertain significance.
Frequency
Consequence
NM_153229.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM92 | ENST00000507382.2 | c.431C>T | p.Pro144Leu | missense_variant | Exon 5 of 5 | 1 | NM_153229.3 | ENSP00000425144.1 | ||
TMEM92 | ENST00000300433.7 | c.431C>T | p.Pro144Leu | missense_variant | Exon 6 of 6 | 1 | ENSP00000300433.3 | |||
TMEM92 | ENST00000511882.1 | n.*143C>T | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152106Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461630Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727146
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.431C>T (p.P144L) alteration is located in exon 6 (coding exon 5) of the TMEM92 gene. This alteration results from a C to T substitution at nucleotide position 431, causing the proline (P) at amino acid position 144 to be replaced by a leucine (L). 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