6-45003745-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001261823.2(SUPT3H):c.-45C>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,760 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001261823.2 5_prime_UTR_premature_start_codon_gain
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 |
---|---|---|---|---|---|---|---|---|
SUPT3H | NM_003599.4 | c.412C>G | p.Gln138Glu | missense_variant | Exon 6 of 11 | ENST00000371459.6 | NP_003590.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SUPT3H | ENST00000371459.6 | c.412C>G | p.Gln138Glu | missense_variant | Exon 6 of 11 | 1 | NM_003599.4 | ENSP00000360514.1 | ||
SUPT3H | ENST00000371460.5 | c.445C>G | p.Gln149Glu | missense_variant | Exon 8 of 13 | 1 | ENSP00000360515.1 | |||
SUPT3H | ENST00000637763.2 | c.226C>G | p.Gln76Glu | missense_variant | Exon 4 of 9 | 3 | ENSP00000490652.2 | |||
SUPT3H | ENST00000475057.5 | n.412C>G | non_coding_transcript_exon_variant | Exon 6 of 12 | 2 | ENSP00000436411.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251016Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135666
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461528Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727056
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74424
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.445C>G (p.Q149E) alteration is located in exon 8 (coding exon 6) of the SUPT3H gene. This alteration results from a C to G substitution at nucleotide position 445, causing the glutamine (Q) at amino acid position 149 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at