rs559821440
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM1BP4_ModerateBS1_Supporting
The NM_000474.4(TWIST1):c.70C>G(p.Pro24Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000261 in 1,457,786 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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. P24L) 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_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TWIST1 | NM_000474.4 | c.70C>G | p.Pro24Ala | missense_variant | 1/2 | ENST00000242261.6 | |
TWIST1 | NR_149001.2 | n.385C>G | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TWIST1 | ENST00000242261.6 | c.70C>G | p.Pro24Ala | missense_variant | 1/2 | 1 | NM_000474.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000264 AC: 4AN: 151658Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 1AN: 83752Hom.: 0 AF XY: 0.0000210 AC XY: 1AN XY: 47638
GnomAD4 exome AF: 0.0000260 AC: 34AN: 1306020Hom.: 0 Cov.: 31 AF XY: 0.0000217 AC XY: 14AN XY: 644436
GnomAD4 genome ? AF: 0.0000264 AC: 4AN: 151766Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74166
ClinVar
Submissions by phenotype
Saethre-Chotzen syndrome;C4551902:TWIST1-related craniosynostosis Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2018 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals with TWIST1-related disease. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the ExAC database. This sequence change replaces proline with alanine at codon 24 of the TWIST1 protein (p.Pro24Ala). The proline residue is moderately conserved and there is a small physicochemical difference between proline and alanine. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at