7-12229791-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001134232.2(TMEM106B):āc.554C>Gā(p.Thr185Ser) variant causes a missense change. The variant allele was found at a frequency of 0.447 in 1,603,674 control chromosomes in the GnomAD database, including 167,361 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001134232.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM106B | NM_001134232.2 | c.554C>G | p.Thr185Ser | missense_variant | 5/8 | ENST00000396668.8 | NP_001127704.1 | |
TMEM106B | NM_018374.4 | c.554C>G | p.Thr185Ser | missense_variant | 6/9 | NP_060844.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM106B | ENST00000396668.8 | c.554C>G | p.Thr185Ser | missense_variant | 5/8 | 1 | NM_001134232.2 | ENSP00000379902.3 |
Frequencies
GnomAD3 genomes AF: 0.505 AC: 76690AN: 151952Hom.: 20473 Cov.: 33
GnomAD3 exomes AF: 0.491 AC: 120502AN: 245634Hom.: 31392 AF XY: 0.488 AC XY: 64705AN XY: 132722
GnomAD4 exome AF: 0.441 AC: 640722AN: 1451604Hom.: 146861 Cov.: 33 AF XY: 0.444 AC XY: 320863AN XY: 722152
GnomAD4 genome AF: 0.505 AC: 76769AN: 152070Hom.: 20500 Cov.: 33 AF XY: 0.507 AC XY: 37668AN XY: 74362
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Leukodystrophy, hypomyelinating, 16 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 10, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at