X-100824151-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001325.3(CSTF2):c.596C>T(p.Thr199Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000413 in 1,210,327 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign 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. T199A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001325.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CSTF2 | NM_001325.3 | c.596C>T | p.Thr199Met | missense_variant | Exon 6 of 14 | ENST00000372972.7 | NP_001316.1 | |
CSTF2 | NM_001306206.2 | c.596C>T | p.Thr199Met | missense_variant | Exon 6 of 15 | NP_001293135.1 | ||
CSTF2 | NM_001306209.2 | c.596C>T | p.Thr199Met | missense_variant | Exon 6 of 14 | NP_001293138.1 | ||
CSTF2 | XM_047441854.1 | c.596C>T | p.Thr199Met | missense_variant | Exon 6 of 10 | XP_047297810.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CSTF2 | ENST00000372972.7 | c.596C>T | p.Thr199Met | missense_variant | Exon 6 of 14 | 1 | NM_001325.3 | ENSP00000362063.2 | ||
CSTF2 | ENST00000415585.7 | c.596C>T | p.Thr199Met | missense_variant | Exon 6 of 15 | 1 | ENSP00000387996.2 | |||
CSTF2 | ENST00000413437.1 | c.569C>T | p.Thr190Met | missense_variant | Exon 6 of 6 | 5 | ENSP00000415705.1 | |||
CSTF2 | ENST00000475126.5 | n.596C>T | non_coding_transcript_exon_variant | Exon 6 of 14 | 5 | ENSP00000432060.1 |
Frequencies
GnomAD3 genomes AF: 0.00000890 AC: 1AN: 112348Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34506
GnomAD3 exomes AF: 0.0000219 AC: 4AN: 182981Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67435
GnomAD4 exome AF: 0.00000364 AC: 4AN: 1097979Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 363345
GnomAD4 genome AF: 0.00000890 AC: 1AN: 112348Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34506
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.596C>T (p.T199M) alteration is located in exon 6 (coding exon 6) of the CSTF2 gene. This alteration results from a C to T substitution at nucleotide position 596, causing the threonine (T) at amino acid position 199 to be replaced by a methionine (M). 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