5-218353-G-C
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000651543.1(ENSG00000286001):n.-3G>C variant causes a non coding transcript exon 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. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000651543.1 non_coding_transcript_exon
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SDHA | NM_004168.4 | c.-3G>C | 5_prime_UTR_variant | Exon 1 of 15 | ENST00000264932.11 | NP_004159.2 | ||
CCDC127 | NM_145265.3 | c.-271C>G | upstream_gene_variant | ENST00000296824.4 | NP_660308.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000286001 | ENST00000651543.1 | n.-3G>C | non_coding_transcript_exon_variant | Exon 1 of 24 | ENSP00000499215.1 | |||||
SDHA | ENST00000264932.11 | c.-3G>C | 5_prime_UTR_variant | Exon 1 of 15 | 1 | NM_004168.4 | ENSP00000264932.6 | |||
ENSG00000286001 | ENST00000651543.1 | n.-3G>C | 5_prime_UTR_variant | Exon 1 of 24 | ENSP00000499215.1 | |||||
CCDC127 | ENST00000296824.4 | c.-271C>G | upstream_gene_variant | 1 | NM_145265.3 | ENSP00000296824.2 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1306702Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 644858
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:1
The c.-3G>C variant is located in the 5' untranslated region (5’ UTR) of the SDHA gene. This variant results from a G to C substitution 3 bases 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