rs10488885
Positions:
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4BS1BS2
The NM_017918.5(MCUB):c.347-1412C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0169 in 151,890 control chromosomes in the GnomAD database, including 32 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 0.017 ( 32 hom., cov: 32)
Consequence
MCUB
NM_017918.5 intron
NM_017918.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.01
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 -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.13).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0169 (2568/151890) while in subpopulation NFE AF= 0.0248 (1688/67964). AF 95% confidence interval is 0.0239. There are 32 homozygotes in gnomad4. There are 1218 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 32 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCUB | NM_017918.5 | c.347-1412C>T | intron_variant | ENST00000394650.7 | |||
MCUB | XM_006714246.4 | c.260-1412C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCUB | ENST00000394650.7 | c.347-1412C>T | intron_variant | 1 | NM_017918.5 | P1 | |||
MCUB | ENST00000472310.5 | n.476-1412C>T | intron_variant, non_coding_transcript_variant | 1 | |||||
MCUB | ENST00000452915.3 | n.442-1412C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0169 AC: 2568AN: 151774Hom.: 32 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0169 AC: 2568AN: 151890Hom.: 32 Cov.: 32 AF XY: 0.0164 AC XY: 1218AN XY: 74212
GnomAD4 genome
?
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2568
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32
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1218
AN XY:
74212
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16
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3476
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