rs73270846
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001371623.1(TCOF1):c.2245C>T(p.Pro749Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00182 in 1,611,454 control chromosomes in the GnomAD database, including 44 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 Benign (★★).
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TCOF1 | NM_001371623.1 | c.2245C>T | p.Pro749Ser | missense_variant | 14/27 | ENST00000643257.2 | NP_001358552.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TCOF1 | ENST00000643257.2 | c.2245C>T | p.Pro749Ser | missense_variant | 14/27 | NM_001371623.1 | ENSP00000493815 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00909 AC: 1384AN: 152186Hom.: 21 Cov.: 34
GnomAD3 exomes AF: 0.00242 AC: 591AN: 243864Hom.: 6 AF XY: 0.00170 AC XY: 224AN XY: 132044
GnomAD4 exome AF: 0.00106 AC: 1551AN: 1459150Hom.: 23 Cov.: 34 AF XY: 0.000938 AC XY: 681AN XY: 725772
GnomAD4 genome AF: 0.00910 AC: 1386AN: 152304Hom.: 21 Cov.: 34 AF XY: 0.00846 AC XY: 630AN XY: 74472
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Sep 01, 2017 | - - |
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | TCOF1: BP4, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 20, 2020 | This variant is associated with the following publications: (PMID: 28065470) - |
Treacher Collins syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 26, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at