5-150396504-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001371623.1(TCOF1):āc.4007A>Gā(p.Lys1336Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.01 in 1,612,838 control chromosomes in the GnomAD database, including 94 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 (ā ā ).
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.4007A>G | p.Lys1336Arg | missense_variant | 24/27 | ENST00000643257.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCOF1 | ENST00000643257.2 | c.4007A>G | p.Lys1336Arg | missense_variant | 24/27 | NM_001371623.1 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00854 AC: 1300AN: 152152Hom.: 8 Cov.: 31
GnomAD3 exomes AF: 0.00853 AC: 2101AN: 246186Hom.: 20 AF XY: 0.00884 AC XY: 1182AN XY: 133642
GnomAD4 exome AF: 0.0102 AC: 14866AN: 1460568Hom.: 86 Cov.: 31 AF XY: 0.0101 AC XY: 7339AN XY: 726520
GnomAD4 genome AF: 0.00853 AC: 1299AN: 152270Hom.: 8 Cov.: 31 AF XY: 0.00907 AC XY: 675AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 15, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2022 | TCOF1: BP4, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 16, 2020 | This variant is associated with the following publications: (PMID: 28065470) - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 02, 2017 | - - |
Treacher Collins syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at