rs150515843
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001371623.1(TCOF1):c.2762C>T(p.Pro921Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000939 in 1,614,178 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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 | UniProt |
---|---|---|---|---|---|---|---|
TCOF1 | NM_001371623.1 | c.2762C>T | p.Pro921Leu | missense_variant | 17/27 | ENST00000643257.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCOF1 | ENST00000643257.2 | c.2762C>T | p.Pro921Leu | missense_variant | 17/27 | NM_001371623.1 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00495 AC: 753AN: 152198Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00119 AC: 300AN: 251198Hom.: 4 AF XY: 0.000943 AC XY: 128AN XY: 135778
GnomAD4 exome AF: 0.000520 AC: 760AN: 1461862Hom.: 7 Cov.: 31 AF XY: 0.000481 AC XY: 350AN XY: 727232
GnomAD4 genome ? AF: 0.00496 AC: 756AN: 152316Hom.: 5 Cov.: 32 AF XY: 0.00483 AC XY: 360AN XY: 74490
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 06, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 04, 2020 | This variant is associated with the following publications: (PMID: 28065470) - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 24, 2018 | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Treacher Collins syndrome 1 Uncertain:1Benign:1
Uncertain significance, no assertion criteria provided | not provided | Genetics Laboratories, Oxford Radcliffe Hospitals NHS Trust | - | - - |
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