chr1-91861488-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003243.5(TGFBR3):c.44C>T(p.Ser15Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,612,018 control chromosomes in the GnomAD database, including 11,638 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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 UniProt.
Frequency
Consequence
NM_003243.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TGFBR3 | NM_003243.5 | c.44C>T | p.Ser15Phe | missense_variant | 2/17 | ENST00000212355.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TGFBR3 | ENST00000212355.9 | c.44C>T | p.Ser15Phe | missense_variant | 2/17 | 1 | NM_003243.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.130 AC: 19741AN: 151990Hom.: 1635 Cov.: 32
GnomAD3 exomes AF: 0.131 AC: 33006AN: 251414Hom.: 3003 AF XY: 0.129 AC XY: 17493AN XY: 135892
GnomAD4 exome AF: 0.100 AC: 146296AN: 1459910Hom.: 9995 Cov.: 30 AF XY: 0.101 AC XY: 73264AN XY: 726348
GnomAD4 genome AF: 0.130 AC: 19782AN: 152108Hom.: 1643 Cov.: 32 AF XY: 0.132 AC XY: 9792AN XY: 74360
ClinVar
Submissions by phenotype
TGFBR3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at