rs915432
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001195518.2(MICU1):c.933+41A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000696 in 1,552,084 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000092 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000067 ( 0 hom. )
Consequence
MICU1
NM_001195518.2 intron
NM_001195518.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.440
Genes affected
MICU1 (HGNC:1530): (mitochondrial calcium uptake 1) This gene encodes an essential regulator of mitochondrial Ca2+ uptake under basal conditions. The encoded protein interacts with the mitochondrial calcium uniporter, a mitochondrial inner membrane Ca2+ channel, and is essential in preventing mitochondrial Ca2+ overload, which can cause excessive production of reactive oxygen species and cell stress. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Mar 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MICU1 | NM_001195518.2 | c.933+41A>T | intron_variant | ENST00000361114.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MICU1 | ENST00000361114.10 | c.933+41A>T | intron_variant | 1 | NM_001195518.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 152034Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000279 AC: 53AN: 190168Hom.: 0 AF XY: 0.000298 AC XY: 30AN XY: 100754
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GnomAD4 exome AF: 0.0000671 AC: 94AN: 1399932Hom.: 0 Cov.: 24 AF XY: 0.0000780 AC XY: 54AN XY: 692736
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GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74366
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ClinVar
Not reported inComputational scores
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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