9-99105255-TGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGC

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2

The NM_004612.4(TGFBR1):​c.76_78dupGCG​(p.Ala26dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00132 in 1,043,488 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00086 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0014 ( 2 hom. )

Consequence

TGFBR1
NM_004612.4 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:12

Conservation

PhyloP100: 0.987
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6
Variant 9-99105255-T-TGGC is Benign according to our data. Variant chr9-99105255-T-TGGC is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 213864.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Benign=1, Likely_benign=8}.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000856 (122/142522) while in subpopulation SAS AF= 0.0026 (12/4608). AF 95% confidence interval is 0.0015. There are 0 homozygotes in gnomad4. There are 61 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High AC in GnomAd4 at 122 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TGFBR1NM_004612.4 linkc.76_78dupGCG p.Ala26dup conservative_inframe_insertion Exon 1 of 9 ENST00000374994.9 NP_004603.1 P36897-1Q5T7S2B4DXN7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TGFBR1ENST00000374994.9 linkc.76_78dupGCG p.Ala26dup conservative_inframe_insertion Exon 1 of 9 1 NM_004612.4 ENSP00000364133.4 P36897-1

Frequencies

GnomAD3 genomes
AF:
0.000857
AC:
122
AN:
142420
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.000689
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000275
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00227
Gnomad SAS
AF:
0.00260
Gnomad FIN
AF:
0.000614
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000928
Gnomad OTH
AF:
0.00153
GnomAD3 exomes
AF:
0.00171
AC:
1
AN:
584
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
340
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00246
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00139
AC:
1255
AN:
900966
Hom.:
2
Cov.:
7
AF XY:
0.00141
AC XY:
596
AN XY:
422760
show subpopulations
Gnomad4 AFR exome
AF:
0.00115
Gnomad4 AMR exome
AF:
0.000713
Gnomad4 ASJ exome
AF:
0.000137
Gnomad4 EAS exome
AF:
0.00109
Gnomad4 SAS exome
AF:
0.00205
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00140
Gnomad4 OTH exome
AF:
0.00166
GnomAD4 genome
AF:
0.000856
AC:
122
AN:
142522
Hom.:
0
Cov.:
30
AF XY:
0.000879
AC XY:
61
AN XY:
69398
show subpopulations
Gnomad4 AFR
AF:
0.000687
Gnomad4 AMR
AF:
0.000275
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00228
Gnomad4 SAS
AF:
0.00260
Gnomad4 FIN
AF:
0.000614
Gnomad4 NFE
AF:
0.000928
Gnomad4 OTH
AF:
0.00151

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:12
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not specified Uncertain:1Benign:3
Apr 17, 2019
Genetic Services Laboratory, University of Chicago
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Oct 06, 2023
Athena Diagnostics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Feb 10, 2025
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Variant summary: TGFBR1 c.76_78dupGCG (p.Ala26dup) results in an in-frame duplication that is predicted to duplicate one amino acid into the encoded protein. The variant allele was found at a frequency of 0.0013 in 1045682 control chromosomes in the gnomAD database, including 2 homozygotes. The observed variant frequency is approximately 702 fold of the estimated maximal expected allele frequency for a pathogenic variant in TGFBR1 causing Loeys-Dietz Syndrome phenotype (1.9e-06). The variant, c.76_78dupGCG, has been reported in the literature in an individual with suspected Loeys-Dietz Syndrome (example, Seo_2018), but was also found in healthy controls (Samowitz_2001, Rego_2018). These reports therefore do not provide unequivocal conclusions about association of the variant with Loeys-Dietz Syndrome. Publications also reported experimental evidence evaluating an impact on protein function, and demonstrated no damaging effect for this variant on either targeting to or translocation across the endoplasmic reticulum membrane as well as no impact on TGF-beta signaling (example, Pasche_1999, Pasche_2005). The following publications have been ascertained in the context of this evaluation (PMID: 21461994, 10582683, 16204663, 30487145, 11746979, 29768367, 19401691, 17575241, 15505640, 17613544). ClinVar contains an entry for this variant (Variation ID: 213864). Based on the evidence outlined above, the variant was classified as likely benign. -

Nov 02, 2016
Eurofins Ntd Llc (ga)
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not provided Benign:4
-
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Jan 08, 2021
GeneDx
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 29768367, 30487145, 11746979, 10582683, 16204663) -

-
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Jun 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

TGFBR1: BS1 -

Familial thoracic aortic aneurysm and aortic dissection Benign:3
Feb 02, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jan 15, 2019
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Sep 08, 2020
Ambry Genetics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

TGFBR1-related disorder Benign:1
Mar 11, 2020
PreventionGenetics, part of Exact Sciences
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Multiple self-healing squamous epithelioma Benign:1
May 04, 2023
Molecular Genetics, Royal Melbourne Hospital
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

South Asian population allele frequency is 0.1502% (rs11466445, 12/4610 alleles, 0 homozygotes in gnomAD v2.1). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.5.1, this variant is classified as LIKELY BENIGN. Following criteria are met: BS1 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11466445; hg19: chr9-101867537; API