chr11-65539084-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_001130144.3(LTBP3):c.3908G>A(p.Arg1303His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000799 in 1,250,810 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1303S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001130144.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LTBP3 | NM_001130144.3 | c.3908G>A | p.Arg1303His | missense_variant | 28/28 | ENST00000301873.11 | |
LTBP3 | NM_021070.4 | c.3767G>A | p.Arg1256His | missense_variant | 27/27 | ||
LTBP3 | NM_001164266.1 | c.3416G>A | p.Arg1139His | missense_variant | 27/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LTBP3 | ENST00000301873.11 | c.3908G>A | p.Arg1303His | missense_variant | 28/28 | 2 | NM_001130144.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000799 AC: 10AN: 1250810Hom.: 0 Cov.: 31 AF XY: 0.00000491 AC XY: 3AN XY: 610900
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Brachyolmia-amelogenesis imperfecta syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Nov 01, 2022 | This variant has not been reported in the literature in individuals affected with LTBP3-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 1303 of the LTBP3 protein (p.Arg1303His). - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Aug 15, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at