rs2782
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152299.4(NCAPH2):c.*50T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
NCAPH2
NM_152299.4 3_prime_UTR
NM_152299.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.23
Publications
32 publications found
Genes affected
NCAPH2 (HGNC:25071): (non-SMC condensin II complex subunit H2) This gene encodes one of the non-SMC subunits of the condensin II complex. This complex plays an essential role in mitotic chromosome assembly. Alternate splicing of this gene results in multiple transcript variants.[provided by RefSeq, May 2010]
SCO2 (HGNC:10604): (synthesis of cytochrome C oxidase 2) Cytochrome c oxidase (COX) catalyzes the transfer of electrons from cytochrome c to molecular oxygen, which helps to maintain the proton gradient across the inner mitochondrial membrane that is necessary for aerobic ATP production. Human COX is a multimeric protein complex that requires several assembly factors; this gene encodes one of the COX assembly factors. The encoded protein is a metallochaperone that is involved in the biogenesis of cytochrome c oxidase subunit II. Mutations in this gene are associated with fatal infantile encephalocardiomyopathy and myopia 6. [provided by RefSeq, Oct 2014]
SCO2 Gene-Disease associations (from GenCC):
- cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- Leigh syndromeInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- myopia 6Inheritance: AD Classification: STRONG Submitted by: G2P
- autosomal recessive axonal charcot-marie-tooth disease due to copper metabolism defectInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
34
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1367886Hom.: 0 Cov.: 52 AF XY: 0.00 AC XY: 0AN XY: 671540
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1367886
Hom.:
Cov.:
52
AF XY:
AC XY:
0
AN XY:
671540
African (AFR)
AF:
AC:
0
AN:
31090
American (AMR)
AF:
AC:
0
AN:
34246
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
23542
East Asian (EAS)
AF:
AC:
0
AN:
35448
South Asian (SAS)
AF:
AC:
0
AN:
76112
European-Finnish (FIN)
AF:
AC:
0
AN:
40394
Middle Eastern (MID)
AF:
AC:
0
AN:
5350
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1064888
Other (OTH)
AF:
AC:
0
AN:
56816
GnomAD4 genome
GnomAD4 genome
Cov.:
34
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.