19-41353016-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000660.7(TGFB1):c.29C>T(p.Pro10Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 1,527,994 control chromosomes in the GnomAD database, including 280,580 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P10R) has been classified as Uncertain significance.
Frequency
Consequence
NM_000660.7 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TGFB1 | NM_000660.7 | c.29C>T | p.Pro10Leu | missense_variant | 1/7 | ENST00000221930.6 | |
TGFB1 | XM_011527242.3 | c.29C>T | p.Pro10Leu | missense_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TGFB1 | ENST00000221930.6 | c.29C>T | p.Pro10Leu | missense_variant | 1/7 | 1 | NM_000660.7 | P1 | |
TMEM91 | ENST00000539627.5 | c.-30+1814G>A | intron_variant | 1 | |||||
TGFB1 | ENST00000600196.2 | c.29C>T | p.Pro10Leu | missense_variant | 1/6 | 5 | |||
TGFB1 | ENST00000677934.1 | c.29C>T | p.Pro10Leu | missense_variant | 1/5 |
Frequencies
GnomAD3 genomes ? AF: 0.589 AC: 89408AN: 151872Hom.: 26723 Cov.: 33
GnomAD3 exomes AF: 0.552 AC: 71740AN: 129938Hom.: 19769 AF XY: 0.554 AC XY: 39248AN XY: 70790
GnomAD4 exome AF: 0.606 AC: 834062AN: 1376004Hom.: 253856 Cov.: 55 AF XY: 0.603 AC XY: 409363AN XY: 678490
GnomAD4 genome ? AF: 0.588 AC: 89439AN: 151990Hom.: 26724 Cov.: 33 AF XY: 0.589 AC XY: 43749AN XY: 74304
ClinVar
Submissions by phenotype
not specified Benign:4
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 78% of patients studied by a panel of primary immunodeficiencies. Number of patients: 74. Only high quality variants are reported. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Inflammatory bowel disease, immunodeficiency, and encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 10, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Meckel syndrome, type 10 Benign:1
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 11, 2021 | - - |
Diaphyseal dysplasia Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 10, 2021 | - - |
Cystic fibrosis Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Jul 15, 2008 | - - |
Breast cancer, invasive, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Jul 15, 2008 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at