rs197204
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017918.5(MCUB):c.99+16482C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,904 control chromosomes in the GnomAD database, including 20,937 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 0.52 ( 20937 hom., cov: 31)
Consequence
MCUB
NM_017918.5 intron
NM_017918.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.759
Genes affected
MCUB (HGNC:26076): (mitochondrial calcium uniporter dominant negative subunit beta) Predicted to enable calcium channel inhibitor activity. Predicted to be involved in calcium import into the mitochondrion and mitochondrial calcium ion homeostasis. Located in mitochondrion and nucleoplasm. Is integral component of mitochondrial inner membrane. Part of uniplex complex. [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=-0.83).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCUB | NM_017918.5 | c.99+16482C>G | intron_variant | ENST00000394650.7 | |||
MCUB | XM_006714246.4 | c.12+15901C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCUB | ENST00000394650.7 | c.99+16482C>G | intron_variant | 1 | NM_017918.5 | P1 | |||
MCUB | ENST00000472310.5 | n.228+16482C>G | intron_variant, non_coding_transcript_variant | 1 | |||||
MCUB | ENST00000452915.3 | n.28+15901C>G | intron_variant, non_coding_transcript_variant | 5 | |||||
MCUB | ENST00000515114.3 | n.225+16482C>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.517 AC: 78513AN: 151786Hom.: 20925 Cov.: 31
GnomAD3 genomes
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78513
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.517 AC: 78555AN: 151904Hom.: 20937 Cov.: 31 AF XY: 0.519 AC XY: 38539AN XY: 74254
GnomAD4 genome
?
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78555
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31
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38539
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74254
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1852
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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