rs2255796
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001371623.1(TCOF1):c.640-223G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,018 control chromosomes in the GnomAD database, including 12,357 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.40 ( 12357 hom., cov: 32)
Consequence
TCOF1
NM_001371623.1 intron
NM_001371623.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.706
Genes affected
TCOF1 (HGNC:11654): (treacle ribosome biogenesis factor 1) This gene encodes a nucleolar protein with a LIS1 homology domain. The protein is involved in ribosomal DNA gene transcription through its interaction with upstream binding factor (UBF). Mutations in this gene have been associated with Treacher Collins syndrome, a disorder which includes abnormal craniofacial development. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 5-150371783-G-A is Benign according to our data. Variant chr5-150371783-G-A is described in ClinVar as [Benign]. Clinvar id is 1274744.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| TCOF1 | NM_001371623.1 | c.640-223G>A | intron_variant | Intron 6 of 26 | ENST00000643257.2 | NP_001358552.1 |
Ensembl
Frequencies
GnomAD3 genomes 0.400 AC: 60741AN: 151898Hom.: 12360 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
60741
AN:
151898
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.400 AC: 60762AN: 152018Hom.: 12357 Cov.: 32 AF XY: 0.399 AC XY: 29646AN XY: 74296 show subpopulations
GnomAD4 genome
AF:
AC:
60762
AN:
152018
Hom.:
Cov.:
32
AF XY:
AC XY:
29646
AN XY:
74296
show subpopulations
African (AFR)
AF:
AC:
14340
AN:
41474
American (AMR)
AF:
AC:
5513
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
1710
AN:
3466
East Asian (EAS)
AF:
AC:
2032
AN:
5164
South Asian (SAS)
AF:
AC:
2234
AN:
4812
European-Finnish (FIN)
AF:
AC:
4045
AN:
10572
Middle Eastern (MID)
AF:
AC:
151
AN:
294
European-Non Finnish (NFE)
AF:
AC:
29515
AN:
67942
Other (OTH)
AF:
AC:
840
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1860
3719
5579
7438
9298
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1320
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Oct 16, 2018
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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