5-218354-AC-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004168.4(SDHA):c.-1delC variant causes a start retained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004168.4 start_retained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SDHA | NM_004168.4 | c.-1delC | start_retained_variant | Exon 1 of 15 | ENST00000264932.11 | NP_004159.2 | ||
SDHA | NM_004168.4 | c.-1delC | 5_prime_UTR_variant | Exon 1 of 15 | ENST00000264932.11 | NP_004159.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SDHA | ENST00000264932 | c.-1delC | start_retained_variant | Exon 1 of 15 | 1 | NM_004168.4 | ENSP00000264932.6 | |||
SDHA | ENST00000264932 | c.-1delC | 5_prime_UTR_variant | Exon 1 of 15 | 1 | NM_004168.4 | ENSP00000264932.6 | |||
ENSG00000286001 | ENST00000651543.1 | n.-1delC | start_retained_variant | Exon 1 of 24 | ENSP00000499215.1 | |||||
ENSG00000286001 | ENST00000651543.1 | n.-1delC | non_coding_transcript_exon_variant | Exon 1 of 24 | ENSP00000499215.1 | |||||
ENSG00000286001 | ENST00000651543.1 | n.-1delC | 5_prime_UTR_variant | Exon 1 of 24 | ENSP00000499215.1 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:1
The c.-1delC variant is located in the 5' untranslated region (5’UTR) of the SDHA gene. This variant results from a single nucleotide deletion one nucleotide upstream from the first translated codon. This nucleotide position is not well conserved in available vertebrate species. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at