chr11-85628639-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018480.7(TMEM126B):āc.32A>Cā(p.Lys11Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,536,152 control chromosomes in the GnomAD database, including 1 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 Uncertain significance (ā ).
Frequency
Consequence
NM_018480.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM126B | NM_018480.7 | c.32A>C | p.Lys11Thr | missense_variant | 1/5 | ENST00000358867.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM126B | ENST00000358867.11 | c.32A>C | p.Lys11Thr | missense_variant | 1/5 | 2 | NM_018480.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000309 AC: 43AN: 139334Hom.: 0 AF XY: 0.000371 AC XY: 28AN XY: 75544
GnomAD4 exome AF: 0.000113 AC: 156AN: 1383820Hom.: 1 Cov.: 31 AF XY: 0.000155 AC XY: 106AN XY: 682850
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152332Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74502
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | May 13, 2024 | In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at