rs11466408
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_003238.6(TGFB2):c.644-4C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,074 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003238.6 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TGFB2 | NM_003238.6 | c.644-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000366930.9 | |||
TGFB2 | NM_001135599.4 | c.728-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
TGFB2 | NR_138148.2 | n.2010-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | ||||
TGFB2 | NR_138149.2 | n.2094-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TGFB2 | ENST00000366930.9 | c.644-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003238.6 | P1 | |||
TGFB2 | ENST00000366929.4 | c.728-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
TGFB2 | ENST00000479322.1 | n.128-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 3 | |||||
TGFB2 | ENST00000488793.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250654Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135488
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460894Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726754
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152180Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74346
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 12, 2018 | 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. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 17, 2015 | - - |
Loeys-Dietz syndrome 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 06, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at