chr11-65546473-G-C
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001130144.3(LTBP3):āc.2322C>Gā(p.Tyr774Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000189 in 1,586,552 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. Y774Y) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001130144.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LTBP3 | NM_001130144.3 | c.2322C>G | p.Tyr774Ter | stop_gained | 16/28 | ENST00000301873.11 | |
LTBP3 | NM_021070.4 | c.2322C>G | p.Tyr774Ter | stop_gained | 16/27 | ||
LTBP3 | NM_001164266.1 | c.1971C>G | p.Tyr657Ter | stop_gained | 16/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LTBP3 | ENST00000301873.11 | c.2322C>G | p.Tyr774Ter | stop_gained | 16/28 | 2 | NM_001130144.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000490 AC: 1AN: 204098Hom.: 0 AF XY: 0.00000882 AC XY: 1AN XY: 113360
GnomAD4 exome AF: 0.00000139 AC: 2AN: 1434320Hom.: 0 Cov.: 31 AF XY: 0.00000281 AC XY: 2AN XY: 712676
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Submissions by phenotype
Brachyolmia-amelogenesis imperfecta syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2009 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at