17-10680847-A-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004589.4(SCO1):c.*272T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0167 in 506,918 control chromosomes in the GnomAD database, including 490 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.039 ( 375 hom., cov: 33)
Exomes 𝑓: 0.0071 ( 115 hom. )
Consequence
SCO1
NM_004589.4 3_prime_UTR
NM_004589.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.23
Genes affected
SCO1 (HGNC:10603): (synthesis of cytochrome C oxidase 1) Mammalian cytochrome c oxidase (COX) catalyzes the transfer of reducing equivalents from cytochrome c to molecular oxygen and pumps protons across the inner mitochondrial membrane. In yeast, 2 related COX assembly genes, SCO1 and SCO2 (synthesis of cytochrome c oxidase), enable subunits 1 and 2 to be incorporated into the holoprotein. This gene is the human homolog to the yeast SCO1 gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 17-10680847-A-G is Benign according to our data. Variant chr17-10680847-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 321788.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCO1 | NM_004589.4 | c.*272T>C | 3_prime_UTR_variant | 6/6 | ENST00000255390.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCO1 | ENST00000255390.10 | c.*272T>C | 3_prime_UTR_variant | 6/6 | 1 | NM_004589.4 | P1 | ||
ENST00000584139.1 | n.114A>G | non_coding_transcript_exon_variant | 1/2 | 3 | |||||
SCO1 | ENST00000577427.1 | c.*272T>C | 3_prime_UTR_variant | 6/6 | 3 | ||||
SCO1 | ENST00000577335.2 | c.*1000T>C | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0388 AC: 5899AN: 152196Hom.: 370 Cov.: 33
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GnomAD4 exome AF: 0.00712 AC: 2525AN: 354604Hom.: 115 Cov.: 3 AF XY: 0.00625 AC XY: 1181AN XY: 188918
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GnomAD4 genome ? AF: 0.0389 AC: 5930AN: 152314Hom.: 375 Cov.: 33 AF XY: 0.0379 AC XY: 2826AN XY: 74486
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Mitochondrial complex IV deficiency, nuclear type 1 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Leigh syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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