chr11-85631730-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_018480.7(TMEM126B):c.125C>T(p.Ser42Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000289 in 1,613,336 control chromosomes in the GnomAD database, including 2 homozygotes. 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 Likely benign (★★).
Frequency
Consequence
NM_018480.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM126B | NM_018480.7 | c.125C>T | p.Ser42Phe | missense_variant | 2/5 | ENST00000358867.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM126B | ENST00000358867.11 | c.125C>T | p.Ser42Phe | missense_variant | 2/5 | 2 | NM_018480.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000289 AC: 44AN: 152100Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000399 AC: 100AN: 250628Hom.: 0 AF XY: 0.000421 AC XY: 57AN XY: 135524
GnomAD4 exome AF: 0.000291 AC: 425AN: 1461118Hom.: 2 Cov.: 31 AF XY: 0.000311 AC XY: 226AN XY: 726884
GnomAD4 genome AF: 0.000269 AC: 41AN: 152218Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74416
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 27, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 21, 2024 | See Variant Classification Assertion Criteria. - |
TMEM126B-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 10, 2021 | This variant is classified as likely 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