chr12-10172529-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001079815.2(TMEM52B):c.-95+1678C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 155,756 control chromosomes in the GnomAD database, including 10,994 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 ( 10765 hom., cov: 32)
Exomes 𝑓: 0.33 ( 229 hom. )
Consequence
TMEM52B
NM_001079815.2 intron
NM_001079815.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.400
Genes affected
TMEM52B (HGNC:26438): (transmembrane protein 52B) Located in extracellular exosome. [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=-0.88).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM52B | NM_001079815.2 | c.-95+1678C>T | intron_variant | ||||
TMEM52B | NM_001384894.1 | c.-311+113C>T | intron_variant | ||||
TMEM52B | NM_001384895.1 | c.-95+113C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM52B | ENST00000381923.6 | c.-95+1678C>T | intron_variant | 5 | P1 | ||||
TMEM52B | ENST00000545924.1 | n.123+1678C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.371 AC: 56265AN: 151806Hom.: 10744 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.327 AC: 1255AN: 3834Hom.: 229 AF XY: 0.326 AC XY: 656AN XY: 2010
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GnomAD4 genome ? AF: 0.371 AC: 56330AN: 151922Hom.: 10765 Cov.: 32 AF XY: 0.375 AC XY: 27805AN XY: 74244
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at