6-45020557-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_003599.4(SUPT3H):c.262C>T(p.Arg88Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000267 in 1,609,676 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. R88H) has been classified as Uncertain significance.
Frequency
Consequence
NM_003599.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SUPT3H | NM_003599.4 | c.262C>T | p.Arg88Cys | missense_variant | 4/11 | ENST00000371459.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUPT3H | ENST00000371459.6 | c.262C>T | p.Arg88Cys | missense_variant | 4/11 | 1 | NM_003599.4 | P1 | |
SUPT3H | ENST00000371460.5 | c.295C>T | p.Arg99Cys | missense_variant | 6/13 | 1 | |||
SUPT3H | ENST00000637763.2 | c.76C>T | p.Arg26Cys | missense_variant | 2/9 | 3 | |||
SUPT3H | ENST00000475057.5 | c.262C>T | p.Arg88Cys | missense_variant, NMD_transcript_variant | 4/12 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151814Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000320 AC: 8AN: 249758Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135070
GnomAD4 exome AF: 0.0000254 AC: 37AN: 1457862Hom.: 0 Cov.: 30 AF XY: 0.0000234 AC XY: 17AN XY: 725218
GnomAD4 genome AF: 0.0000395 AC: 6AN: 151814Hom.: 0 Cov.: 32 AF XY: 0.0000405 AC XY: 3AN XY: 74142
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 16, 2023 | The c.295C>T (p.R99C) alteration is located in exon 6 (coding exon 4) of the SUPT3H gene. This alteration results from a C to T substitution at nucleotide position 295, causing the arginine (R) at amino acid position 99 to be replaced by a cysteine (C). 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