rs1800470
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 (★★).
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TGFB1 | NM_000660.7 | c.29C>T | p.Pro10Leu | missense_variant | Exon 1 of 7 | ENST00000221930.6 | NP_000651.3 | |
TGFB1 | XM_011527242.3 | c.29C>T | p.Pro10Leu | missense_variant | Exon 1 of 7 | XP_011525544.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TGFB1 | ENST00000221930.6 | c.29C>T | p.Pro10Leu | missense_variant | Exon 1 of 7 | 1 | NM_000660.7 | ENSP00000221930.4 |
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
- -
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. -
- -
- -
not provided Benign:2
- -
- -
Inflammatory bowel disease, immunodeficiency, and encephalopathy Benign:1
- -
Meckel syndrome, type 10 Benign:1
- -
Diaphyseal dysplasia Benign:1
- -
Cystic fibrosis Other:1
- -
Breast cancer, invasive, susceptibility to Other:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at