chr11-87321245-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_022918.4(TMEM135):c.1289G>C(p.Gly430Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0294 in 1,613,404 control chromosomes in the GnomAD database, including 1,433 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_022918.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM135 | NM_022918.4 | c.1289G>C | p.Gly430Ala | missense_variant | 15/15 | ENST00000305494.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM135 | ENST00000305494.6 | c.1289G>C | p.Gly430Ala | missense_variant | 15/15 | 1 | NM_022918.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0287 AC: 4363AN: 151976Hom.: 135 Cov.: 32
GnomAD3 exomes AF: 0.0411 AC: 10322AN: 251126Hom.: 459 AF XY: 0.0430 AC XY: 5839AN XY: 135740
GnomAD4 exome AF: 0.0295 AC: 43123AN: 1461312Hom.: 1298 Cov.: 31 AF XY: 0.0313 AC XY: 22728AN XY: 726982
GnomAD4 genome ? AF: 0.0287 AC: 4372AN: 152092Hom.: 135 Cov.: 32 AF XY: 0.0303 AC XY: 2251AN XY: 74344
ClinVar
Submissions by phenotype
TMEM135-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 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