6-33700261-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_032340.4(UQCC2):c.283+183C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0519 in 152,046 control chromosomes in the GnomAD database, including 343 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.052 ( 343 hom., cov: 33)
Consequence
UQCC2
NM_032340.4 intron
NM_032340.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.360
Genes affected
UQCC2 (HGNC:21237): (ubiquinol-cytochrome c reductase complex assembly factor 2) This gene encodes a nucleoid protein localized to the mitochondria inner membrane. The encoded protein affects regulation of insulin secretion, mitochondrial ATP production, and myogenesis through modulation of mitochondrial respiratory chain activity. [provided by RefSeq, Oct 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant 6-33700261-G-A is Benign according to our data. Variant chr6-33700261-G-A is described in ClinVar as [Benign]. Clinvar id is 684316.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UQCC2 | NM_032340.4 | c.283+183C>T | intron_variant | ENST00000607484.6 | NP_115716.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UQCC2 | ENST00000607484.6 | c.283+183C>T | intron_variant | 1 | NM_032340.4 | ENSP00000476140 | P1 | |||
UQCC2 | ENST00000374214.3 | c.208+183C>T | intron_variant | 5 | ENSP00000363331 | |||||
UQCC2 | ENST00000374231.8 | c.281+183C>T | intron_variant | 3 | ENSP00000363348 |
Frequencies
GnomAD3 genomes AF: 0.0517 AC: 7861AN: 151928Hom.: 338 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: 0.0519 AC: 7897AN: 152046Hom.: 343 Cov.: 33 AF XY: 0.0520 AC XY: 3861AN XY: 74306
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational 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