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
Consequence
NM_004612.4 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000857 AC: 122AN: 142420Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00171 AC: 1AN: 584Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 340
GnomAD4 exome AF: 0.00139 AC: 1255AN: 900966Hom.: 2 Cov.: 7 AF XY: 0.00141 AC XY: 596AN XY: 422760
GnomAD4 genome AF: 0.000856 AC: 122AN: 142522Hom.: 0 Cov.: 30 AF XY: 0.000879 AC XY: 61AN XY: 69398
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:3
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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. -
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not provided Benign:4
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This variant is associated with the following publications: (PMID: 29768367, 30487145, 11746979, 10582683, 16204663) -
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TGFBR1: BS1 -
Familial thoracic aortic aneurysm and aortic dissection Benign:3
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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
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
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at