5-218352-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004168.4(SDHA):c.-4A>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,120 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004168.4 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SDHA | NM_004168.4 | c.-4A>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 15 | ENST00000264932.11 | NP_004159.2 | ||
SDHA | NM_004168.4 | c.-4A>T | 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.-4A>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 15 | 1 | NM_004168.4 | ENSP00000264932.6 | |||
SDHA | ENST00000264932 | c.-4A>T | 5_prime_UTR_variant | Exon 1 of 15 | 1 | NM_004168.4 | ENSP00000264932.6 | |||
ENSG00000286001 | ENST00000651543.1 | n.-4A>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 24 | ENSP00000499215.1 | |||||
ENSG00000286001 | ENST00000651543.1 | n.-4A>T | non_coding_transcript_exon_variant | Exon 1 of 24 | ENSP00000499215.1 | |||||
ENSG00000286001 | ENST00000651543.1 | n.-4A>T | 5_prime_UTR_variant | Exon 1 of 24 | ENSP00000499215.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152120Hom.: 0 Cov.: 34
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1306410Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 644660
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152120Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74310
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:1
The c.-4A>T variant is located in the 5' untranslated region (5’ UTR) of the SDHA gene. This variant results from an A to T substitution 4 bases upstream from the first translated codon. This nucleotide position is not well conserved in available vertebrate species. Based on the available evidence, the clinical significance of this variant remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at