chr11-87038071-C-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_022918.4(TMEM135):c.26C>G(p.Pro9Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000515 in 1,614,206 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0030 ( 4 hom., cov: 31)
Exomes 𝑓: 0.00026 ( 3 hom. )
Consequence
TMEM135
NM_022918.4 missense
NM_022918.4 missense
Scores
1
8
8
Clinical Significance
Conservation
PhyloP100: 5.35
Genes affected
TMEM135 (HGNC:26167): (transmembrane protein 135) Predicted to be involved in peroxisome organization. Predicted to act upstream of or within response to cold and response to food. Predicted to be located in mitochondrion and peroxisome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.00823316).
BP6
?
Variant 11-87038071-C-G is Benign according to our data. Variant chr11-87038071-C-G is described in ClinVar as [Benign]. Clinvar id is 3053201.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM135 | NM_022918.4 | c.26C>G | p.Pro9Arg | missense_variant | 1/15 | ENST00000305494.6 | |
TMEM135 | NM_001168724.2 | c.26C>G | p.Pro9Arg | missense_variant | 1/14 | ||
TMEM135 | NR_033149.2 | n.138C>G | non_coding_transcript_exon_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM135 | ENST00000305494.6 | c.26C>G | p.Pro9Arg | missense_variant | 1/15 | 1 | NM_022918.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00296 AC: 451AN: 152204Hom.: 4 Cov.: 31
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GnomAD3 exomes AF: 0.000771 AC: 194AN: 251480Hom.: 1 AF XY: 0.000522 AC XY: 71AN XY: 135914
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GnomAD4 exome AF: 0.000260 AC: 380AN: 1461884Hom.: 3 Cov.: 32 AF XY: 0.000209 AC XY: 152AN XY: 727246
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GnomAD4 genome ? AF: 0.00296 AC: 451AN: 152322Hom.: 4 Cov.: 31 AF XY: 0.00309 AC XY: 230AN XY: 74484
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
TMEM135-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 01, 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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;D;D;T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;.;M
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;N;D
REVEL
Benign
Sift
Uncertain
D;D;T;D
Sift4G
Uncertain
D;D;D;T
Polyphen
P;.;.;D
Vest4
MVP
MPC
0.69
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at