9-99105255-TGGCGGCGGC-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_004612.4(TGFBR1):c.70_78delGCGGCGGCG(p.Ala24_Ala26del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0928 in 1,043,304 control chromosomes in the GnomAD database, including 4,897 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004612.4 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0815 AC: 11610AN: 142372Hom.: 586 Cov.: 30
GnomAD3 exomes AF: 0.0582 AC: 34AN: 584Hom.: 1 AF XY: 0.0765 AC XY: 26AN XY: 340
GnomAD4 exome AF: 0.0946 AC: 85196AN: 900830Hom.: 4312 AF XY: 0.0941 AC XY: 39758AN XY: 422658
GnomAD4 genome AF: 0.0815 AC: 11615AN: 142474Hom.: 585 Cov.: 30 AF XY: 0.0812 AC XY: 5633AN XY: 69374
ClinVar
Submissions by phenotype
not specified Benign:5
BA1, BS1, BP3, BP6; This alteration has an allele frequency that is greater than 5% healthy populations (ExAC/gnomAD), has an allele frequency that is greater than expected for the associated disease, is an in-frame deletion/insertion in a repetitive region without a known function, and was reported as a benign/likely benign alteration by a reputable source (ClinVar or other correspondence from a clinical testing laboratory). -
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Familial thoracic aortic aneurysm and aortic dissection Benign:4
This alteration is classified as 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. -
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This alteration is classified as benign based on a combination of the following: 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. -
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Loeys-Dietz syndrome 1 Uncertain:1Benign:1
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Loeys-Dietz syndrome Benign:2
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not provided Benign:2
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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Ehlers-Danlos syndrome Benign:1
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Thoracic aortic aneurysm Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at