rs75583421
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001371623.1(TCOF1):c.1783G>A(p.Val595Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00956 in 1,614,248 control chromosomes in the GnomAD database, including 102 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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.1783G>A | p.Val595Ile | missense_variant | 12/27 | ENST00000643257.2 | NP_001358552.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TCOF1 | ENST00000643257.2 | c.1783G>A | p.Val595Ile | missense_variant | 12/27 | NM_001371623.1 | ENSP00000493815 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00784 AC: 1194AN: 152244Hom.: 10 Cov.: 34
GnomAD3 exomes AF: 0.00746 AC: 1875AN: 251374Hom.: 10 AF XY: 0.00741 AC XY: 1007AN XY: 135864
GnomAD4 exome AF: 0.00973 AC: 14231AN: 1461886Hom.: 92 Cov.: 35 AF XY: 0.00960 AC XY: 6983AN XY: 727242
GnomAD4 genome AF: 0.00784 AC: 1194AN: 152362Hom.: 10 Cov.: 34 AF XY: 0.00809 AC XY: 603AN XY: 74512
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2024 | TCOF1: BP4, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 05, 2020 | This variant is associated with the following publications: (PMID: 28065470) - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 13, 2017 | - - |
Treacher Collins syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at