17-50278887-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153229.3(TMEM92):c.257C>T(p.Pro86Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000626 in 1,613,700 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_153229.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM92 | ENST00000507382.2 | c.257C>T | p.Pro86Leu | missense_variant | Exon 4 of 5 | 1 | NM_153229.3 | ENSP00000425144.1 | ||
TMEM92 | ENST00000300433.7 | c.257C>T | p.Pro86Leu | missense_variant | Exon 5 of 6 | 1 | ENSP00000300433.3 | |||
TMEM92 | ENST00000511882.1 | n.353C>T | non_coding_transcript_exon_variant | Exon 4 of 4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151940Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251280Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135804
GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461760Hom.: 0 Cov.: 32 AF XY: 0.0000701 AC XY: 51AN XY: 727204
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151940Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74188
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.257C>T (p.P86L) alteration is located in exon 5 (coding exon 4) of the TMEM92 gene. This alteration results from a C to T substitution at nucleotide position 257, causing the proline (P) at amino acid position 86 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