rs2014286
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_181723.3(MICU3):c.382-14468G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 518,112 control chromosomes in the GnomAD database, including 21,168 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 0.31 ( 11472 hom., cov: 32)
Exomes 𝑓: 0.19 ( 9696 hom. )
Consequence
MICU3
NM_181723.3 intron
NM_181723.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0530
Genes affected
MICU3 (HGNC:27820): (mitochondrial calcium uptake family member 3) Predicted to enable calcium ion binding activity. Predicted to be involved in calcium import into the mitochondrion and mitochondrial calcium ion homeostasis. Predicted to be located in mitochondrial inner membrane. Predicted to be 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=-0.88).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MICU3 | NM_181723.3 | c.382-14468G>A | intron_variant | ENST00000318063.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MICU3 | ENST00000318063.10 | c.382-14468G>A | intron_variant | 1 | NM_181723.3 | P1 | |||
MICU3 | ENST00000522235.5 | n.84-14468G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.313 AC: 47573AN: 151912Hom.: 11446 Cov.: 32
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GnomAD3 exomes AF: 0.235 AC: 53699AN: 228426Hom.: 9571 AF XY: 0.218 AC XY: 27500AN XY: 126254
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GnomAD4 exome AF: 0.193 AC: 70756AN: 366084Hom.: 9696 Cov.: 0 AF XY: 0.183 AC XY: 38396AN XY: 209906
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GnomAD4 genome ? AF: 0.313 AC: 47648AN: 152028Hom.: 11472 Cov.: 32 AF XY: 0.309 AC XY: 22991AN XY: 74294
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at