chr12-128297477-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001136103.3(TMEM132C):c.85+29990C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0925 in 152,214 control chromosomes in the GnomAD database, including 787 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 0.093 ( 787 hom., cov: 33)
Consequence
TMEM132C
NM_001136103.3 intron
NM_001136103.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.669
Genes affected
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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=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM132C | NM_001136103.3 | c.85+29990C>T | intron_variant | ENST00000435159.3 | NP_001129575.2 | |||
TMEM132C | NM_001387058.1 | c.25+29183C>T | intron_variant | NP_001373987.1 | ||||
TMEM132C | XM_047429886.1 | c.85+29990C>T | intron_variant | XP_047285842.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0926 AC: 14081AN: 152094Hom.: 784 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0925 AC: 14087AN: 152214Hom.: 787 Cov.: 33 AF XY: 0.0936 AC XY: 6967AN XY: 74430
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779
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3478
ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at