7-19116759-G-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP3_Moderate
The NM_000474.4(TWIST1):c.563C>G(p.Ser188Trp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,956 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S188L) has been classified as Uncertain significance.
Frequency
Consequence
NM_000474.4 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 |
---|---|---|---|---|---|---|---|
TWIST1 | NM_000474.4 | c.563C>G | p.Ser188Trp | missense_variant | 1/2 | ENST00000242261.6 | |
TWIST1 | NR_149001.2 | n.878C>G | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TWIST1 | ENST00000242261.6 | c.563C>G | p.Ser188Trp | missense_variant | 1/2 | 1 | NM_000474.4 | P1 | |
TWIST1 | ENST00000354571.5 | c.362C>G | p.Ser121Trp | missense_variant, NMD_transcript_variant | 1/3 | 2 | |||
TWIST1 | ENST00000443687.5 | c.167C>G | p.Ser56Trp | missense_variant, NMD_transcript_variant | 1/4 | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247634Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134260
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460956Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 726690
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at