rs754898843
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_003239.5(TGFB3):c.519C>T(p.Ile173=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,461,810 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003239.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TGFB3 | NM_003239.5 | c.519C>T | p.Ile173= | splice_region_variant, synonymous_variant | 3/7 | ENST00000238682.8 | |
TGFB3 | NM_001329939.2 | c.519C>T | p.Ile173= | splice_region_variant, synonymous_variant | 4/8 | ||
TGFB3 | NM_001329938.2 | c.519C>T | p.Ile173= | splice_region_variant, synonymous_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TGFB3 | ENST00000238682.8 | c.519C>T | p.Ile173= | splice_region_variant, synonymous_variant | 3/7 | 1 | NM_003239.5 | P1 | |
TGFB3-AS1 | ENST00000553732.1 | n.330G>A | non_coding_transcript_exon_variant | 1/2 | 4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251298Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135818
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461810Hom.: 1 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727202
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2020 | - - |
Rienhoff syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 03, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at