rs200327514
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP3BP4_StrongBP6_Very_StrongBS2
The NM_017849.4(TMEM127):c.572C>T(p.Thr191Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000349 in 1,614,134 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T191T) has been classified as Likely benign.
Frequency
Consequence
NM_017849.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM127 | NM_017849.4 | c.572C>T | p.Thr191Met | missense_variant | 4/4 | ENST00000258439.8 | |
TMEM127 | NM_001193304.3 | c.572C>T | p.Thr191Met | missense_variant | 4/4 | ||
TMEM127 | NM_001407282.1 | c.320C>T | p.Thr107Met | missense_variant | 3/3 | ||
TMEM127 | NM_001407283.1 | c.320C>T | p.Thr107Met | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM127 | ENST00000258439.8 | c.572C>T | p.Thr191Met | missense_variant | 4/4 | 1 | NM_017849.4 | P1 | |
TMEM127 | ENST00000432959.1 | c.572C>T | p.Thr191Met | missense_variant | 4/4 | 1 | P1 | ||
TMEM127 | ENST00000435268.1 | c.320C>T | p.Thr107Met | missense_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000736 AC: 112AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000895 AC: 225AN: 251442Hom.: 1 AF XY: 0.000861 AC XY: 117AN XY: 135906
GnomAD4 exome AF: 0.000309 AC: 451AN: 1461888Hom.: 1 Cov.: 32 AF XY: 0.000300 AC XY: 218AN XY: 727246
GnomAD4 genome AF: 0.000736 AC: 112AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.00117 AC XY: 87AN XY: 74442
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 15, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Benign, criteria provided, single submitter | curation | Sema4, Sema4 | Aug 23, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Feb 23, 2023 | - - |
Hereditary pheochromocytoma-paraganglioma Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 10, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at