rs114326915
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001371623.1(TCOF1):c.1229C>T(p.Ser410Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00218 in 1,612,552 control chromosomes in the GnomAD database, including 58 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S410P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001371623.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCOF1 | NM_001371623.1 | c.1229C>T | p.Ser410Leu | missense_variant | 9/27 | ENST00000643257.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCOF1 | ENST00000643257.2 | c.1229C>T | p.Ser410Leu | missense_variant | 9/27 | NM_001371623.1 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0114 AC: 1727AN: 151010Hom.: 31 Cov.: 34
GnomAD3 exomes AF: 0.00304 AC: 756AN: 248284Hom.: 10 AF XY: 0.00217 AC XY: 292AN XY: 134440
GnomAD4 exome AF: 0.00121 AC: 1771AN: 1461420Hom.: 27 Cov.: 33 AF XY: 0.00104 AC XY: 756AN XY: 727006
GnomAD4 genome ? AF: 0.0115 AC: 1737AN: 151132Hom.: 31 Cov.: 34 AF XY: 0.0109 AC XY: 804AN XY: 73810
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 04, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 17, 2019 | This variant is associated with the following publications: (PMID: 28065470) - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | TCOF1: BP4, BS1, BS2 - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Sep 11, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jul 09, 2020 | - - |
Treacher Collins syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at