1-156285294-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032323.3(TMEM79):c.68C>T(p.Pro23Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000014 in 1,424,480 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_032323.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM79 | NM_032323.3 | c.68C>T | p.Pro23Leu | missense_variant | 2/4 | ENST00000405535.3 | NP_115699.1 | |
SMG5 | NM_001323617.2 | c.-125+1339G>A | intron_variant | NP_001310546.1 | ||||
TMEM79 | NR_026678.2 | n.245C>T | non_coding_transcript_exon_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM79 | ENST00000405535.3 | c.68C>T | p.Pro23Leu | missense_variant | 2/4 | 1 | NM_032323.3 | ENSP00000384748 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000461 AC: 1AN: 216776Hom.: 0 AF XY: 0.00000857 AC XY: 1AN XY: 116646
GnomAD4 exome AF: 0.00000140 AC: 2AN: 1424480Hom.: 0 Cov.: 30 AF XY: 0.00000142 AC XY: 1AN XY: 706362
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 26, 2023 | The c.68C>T (p.P23L) alteration is located in exon 2 (coding exon 1) of the TMEM79 gene. This alteration results from a C to T substitution at nucleotide position 68, causing the proline (P) at amino acid position 23 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