9-99105155-GGC-G
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_004612.4(TGFBR1):c.-50_-49delGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000107 in 933,334 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000011 ( 0 hom. )
Consequence
TGFBR1
NM_004612.4 5_prime_UTR
NM_004612.4 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.443
Publications
0 publications found
Genes affected
TGFBR1 (HGNC:11772): (transforming growth factor beta receptor 1) The protein encoded by this gene forms a heteromeric complex with type II TGF-beta receptors when bound to TGF-beta, transducing the TGF-beta signal from the cell surface to the cytoplasm. The encoded protein is a serine/threonine protein kinase. Mutations in this gene have been associated with Loeys-Dietz aortic aneurysm syndrome (LDAS). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]
TGFBR1 Gene-Disease associations (from GenCC):
- familial thoracic aortic aneurysm and aortic dissectionInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen
- Loeys-Dietz syndromeInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen
- Loeys-Dietz syndrome 1Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, PanelApp Australia, Genomics England PanelApp, G2P
- multiple self-healing squamous epitheliomaInheritance: AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 9-99105155-GGC-G is Benign according to our data. Variant chr9-99105155-GGC-G is described in ClinVar as [Benign]. Clinvar id is 213859.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000107 AC: 1AN: 933334Hom.: 0 AF XY: 0.00000230 AC XY: 1AN XY: 435722 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
933334
Hom.:
AF XY:
AC XY:
1
AN XY:
435722
show subpopulations
African (AFR)
AF:
AC:
0
AN:
18716
American (AMR)
AF:
AC:
0
AN:
3698
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
9318
East Asian (EAS)
AF:
AC:
0
AN:
14242
South Asian (SAS)
AF:
AC:
0
AN:
18180
European-Finnish (FIN)
AF:
AC:
0
AN:
7804
Middle Eastern (MID)
AF:
AC:
0
AN:
2170
European-Non Finnish (NFE)
AF:
AC:
1
AN:
825074
Other (OTH)
AF:
AC:
0
AN:
34132
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Jun 30, 2015
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
This variant was found in TAADV2-PANCARD -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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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