rs14978
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001134232.2(TMEM106B):c.*1551A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 150,740 control chromosomes in the GnomAD database, including 10,707 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.37 ( 10706 hom., cov: 29)
Exomes 𝑓: 0.75 ( 1 hom. )
Consequence
TMEM106B
NM_001134232.2 3_prime_UTR
NM_001134232.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.93
Genes affected
TMEM106B (HGNC:22407): (transmembrane protein 106B) Enables ATPase binding activity. Involved in dendrite morphogenesis and lysosome localization. Located in endosome and lysosomal membrane. Implicated in hypomyelinating leukodystrophy. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM106B | NM_001134232.2 | c.*1551A>G | 3_prime_UTR_variant | 8/8 | ENST00000396668.8 | ||
TMEM106B | NM_018374.4 | c.*1551A>G | 3_prime_UTR_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM106B | ENST00000396668.8 | c.*1551A>G | 3_prime_UTR_variant | 8/8 | 1 | NM_001134232.2 | P1 | ||
TMEM106B | ENST00000396667.7 | c.*1551A>G | 3_prime_UTR_variant | 9/9 | 1 | P1 | |||
TMEM106B | ENST00000444443.6 | c.*1551A>G | 3_prime_UTR_variant | 8/8 | 4 | P1 | |||
TMEM106B | ENST00000704417.1 | c.*1551A>G | 3_prime_UTR_variant | 8/8 |
Frequencies
GnomAD3 genomes ? AF: 0.370 AC: 55759AN: 150622Hom.: 10690 Cov.: 29
GnomAD3 genomes
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29
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GnomAD4 exome AF: 0.750 AC: 3AN: 4Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3AN XY: 4
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GnomAD4 genome ? AF: 0.370 AC: 55816AN: 150736Hom.: 10706 Cov.: 29 AF XY: 0.373 AC XY: 27425AN XY: 73620
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at