rs145100473
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM1BP4_ModerateBP6BS2
The NM_005138.3(SCO2):c.341G>A(p.Arg114His) variant causes a missense change. The variant allele was found at a frequency of 0.000394 in 1,613,244 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_005138.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCO2 | ENST00000395693.8 | c.341G>A | p.Arg114His | missense_variant | Exon 2 of 2 | 1 | NM_005138.3 | ENSP00000379046.4 | ||
NCAPH2 | ENST00000420993.7 | c.*696C>T | 3_prime_UTR_variant | Exon 20 of 20 | 1 | NM_152299.4 | ENSP00000410088.2 |
Frequencies
GnomAD3 genomes AF: 0.000789 AC: 120AN: 152174Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000831 AC: 208AN: 250450Hom.: 1 AF XY: 0.000789 AC XY: 107AN XY: 135664
GnomAD4 exome AF: 0.000354 AC: 517AN: 1460952Hom.: 6 Cov.: 73 AF XY: 0.000376 AC XY: 273AN XY: 726792
GnomAD4 genome AF: 0.000781 AC: 119AN: 152292Hom.: 1 Cov.: 33 AF XY: 0.00105 AC XY: 78AN XY: 74460
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
SCO2: BS2 -
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 27581939, 25959673, 34426522, 23643385, 35457050, 28518168, 35328081, 32461654) -
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Myopia 6 Pathogenic:1
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Mitochondrial complex IV deficiency, nuclear type 1 Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at