17-50278946-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153229.3(TMEM92):c.316C>A(p.Pro106Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 152,054 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
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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.316C>A | p.Pro106Thr | missense_variant | Exon 4 of 5 | 1 | NM_153229.3 | ENSP00000425144.1 | ||
TMEM92 | ENST00000300433.7 | c.316C>A | p.Pro106Thr | missense_variant | Exon 5 of 6 | 1 | ENSP00000300433.3 | |||
TMEM92 | ENST00000511882.1 | n.412C>A | non_coding_transcript_exon_variant | Exon 4 of 4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152054Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250520Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135432
GnomAD4 exome Cov.: 33
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152054Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74266
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.316C>A (p.P106T) alteration is located in exon 5 (coding exon 4) of the TMEM92 gene. This alteration results from a C to A substitution at nucleotide position 316, causing the proline (P) at amino acid position 106 to be replaced by a threonine (T). 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