NM_004168.4:c.-61T>A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004168.4(SDHA):c.-61T>A variant causes a upstream gene 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
SDHA
NM_004168.4 upstream_gene
NM_004168.4 upstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0520
Publications
0 publications found
Genes affected
SDHA (HGNC:10680): (succinate dehydrogenase complex flavoprotein subunit A) This gene encodes a major catalytic subunit of succinate-ubiquinone oxidoreductase, a complex of the mitochondrial respiratory chain. The complex is composed of four nuclear-encoded subunits and is localized in the mitochondrial inner membrane. Mutations in this gene have been associated with a form of mitochondrial respiratory chain deficiency known as Leigh Syndrome. A pseudogene has been identified on chromosome 3q29. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2014]
CCDC127 (HGNC:30520): (coiled-coil domain containing 127) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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=-0.77).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SDHA | NM_004168.4 | c.-61T>A | upstream_gene_variant | ENST00000264932.11 | NP_004159.2 | |||
CCDC127 | NM_145265.3 | c.-213A>T | upstream_gene_variant | ENST00000296824.4 | NP_660308.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SDHA | ENST00000264932.11 | c.-61T>A | upstream_gene_variant | 1 | NM_004168.4 | ENSP00000264932.6 | ||||
CCDC127 | ENST00000296824.4 | c.-213A>T | upstream_gene_variant | 1 | NM_145265.3 | ENSP00000296824.2 | ||||
ENSG00000286001 | ENST00000651543.1 | n.-61T>A | upstream_gene_variant | ENSP00000499215.1 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 genomes
Cov.:
34
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1273984Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 626550
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1273984
Hom.:
Cov.:
28
AF XY:
AC XY:
0
AN XY:
626550
African (AFR)
AF:
AC:
0
AN:
25678
American (AMR)
AF:
AC:
0
AN:
20124
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
20228
East Asian (EAS)
AF:
AC:
0
AN:
29766
South Asian (SAS)
AF:
AC:
0
AN:
63242
European-Finnish (FIN)
AF:
AC:
0
AN:
32522
Middle Eastern (MID)
AF:
AC:
0
AN:
3614
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1026848
Other (OTH)
AF:
AC:
0
AN:
51962
GnomAD4 genome Cov.: 34
GnomAD4 genome
Cov.:
34
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
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