11-87302351-T-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_022918.4(TMEM135):c.607T>C(p.Tyr203His) variant causes a missense change. The variant allele was found at a frequency of 0.000718 in 1,613,858 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y203C) has been classified as Uncertain significance.
Frequency
Consequence
NM_022918.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM135 | NM_022918.4 | c.607T>C | p.Tyr203His | missense_variant | 8/15 | ENST00000305494.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM135 | ENST00000305494.6 | c.607T>C | p.Tyr203His | missense_variant | 8/15 | 1 | NM_022918.4 | P1 | |
TMEM135 | ENST00000340353.11 | c.541T>C | p.Tyr181His | missense_variant | 7/14 | 1 | |||
TMEM135 | ENST00000532959.5 | c.220T>C | p.Tyr74His | missense_variant | 5/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00402 AC: 612AN: 152110Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000959 AC: 241AN: 251296Hom.: 0 AF XY: 0.000766 AC XY: 104AN XY: 135812
GnomAD4 exome AF: 0.000369 AC: 540AN: 1461626Hom.: 2 Cov.: 31 AF XY: 0.000334 AC XY: 243AN XY: 727118
GnomAD4 genome ? AF: 0.00406 AC: 618AN: 152232Hom.: 3 Cov.: 32 AF XY: 0.00376 AC XY: 280AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
TMEM135-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 14, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at