6-45020556-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_003599.4(SUPT3H):c.263G>A(p.Arg88His) variant causes a missense change. The variant allele was found at a frequency of 0.000018 in 1,609,706 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R88C) has been classified as Uncertain significance.
Frequency
Consequence
NM_003599.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SUPT3H | NM_003599.4 | c.263G>A | p.Arg88His | missense_variant | 4/11 | ENST00000371459.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUPT3H | ENST00000371459.6 | c.263G>A | p.Arg88His | missense_variant | 4/11 | 1 | NM_003599.4 | P1 | |
SUPT3H | ENST00000371460.5 | c.296G>A | p.Arg99His | missense_variant | 6/13 | 1 | |||
SUPT3H | ENST00000637763.2 | c.77G>A | p.Arg26His | missense_variant | 2/9 | 3 | |||
SUPT3H | ENST00000475057.5 | c.263G>A | p.Arg88His | missense_variant, NMD_transcript_variant | 4/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151860Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000440 AC: 11AN: 249770Hom.: 0 AF XY: 0.0000592 AC XY: 8AN XY: 135070
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1457846Hom.: 0 Cov.: 29 AF XY: 0.0000276 AC XY: 20AN XY: 725204
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151860Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74150
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 21, 2022 | The c.296G>A (p.R99H) alteration is located in exon 6 (coding exon 4) of the SUPT3H gene. This alteration results from a G to A substitution at nucleotide position 296, causing the arginine (R) at amino acid position 99 to be replaced by a histidine (H). 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