11-65539122-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_001130144.3(LTBP3):c.3870C>T(p.Arg1290=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000982 in 1,476,920 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 Likely benign (★★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
LTBP3
NM_001130144.3 synonymous
NM_001130144.3 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 4.62
Genes affected
LTBP3 (HGNC:6716): (latent transforming growth factor beta binding protein 3) The protein encoded by this gene forms a complex with transforming growth factor beta (TGF-beta) proteins and may be involved in their subcellular localization. Activation of this complex requires removal of the encoded binding protein. This protein also may play a structural role in the extracellular matrix. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 11-65539122-G-A is Benign according to our data. Variant chr11-65539122-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2062501.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LTBP3 | NM_001130144.3 | c.3870C>T | p.Arg1290= | synonymous_variant | 28/28 | ENST00000301873.11 | NP_001123616.1 | |
LTBP3 | NM_021070.4 | c.3729C>T | p.Arg1243= | synonymous_variant | 27/27 | NP_066548.2 | ||
LTBP3 | NM_001164266.1 | c.3378C>T | p.Arg1126= | synonymous_variant | 27/27 | NP_001157738.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LTBP3 | ENST00000301873.11 | c.3870C>T | p.Arg1290= | synonymous_variant | 28/28 | 2 | NM_001130144.3 | ENSP00000301873 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000330 AC: 5AN: 151522Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000272 AC: 29AN: 106424Hom.: 0 AF XY: 0.000371 AC XY: 22AN XY: 59264
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GnomAD4 exome AF: 0.000106 AC: 140AN: 1325290Hom.: 0 Cov.: 31 AF XY: 0.000143 AC XY: 93AN XY: 651276
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GnomAD4 genome AF: 0.0000330 AC: 5AN: 151630Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 74130
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Brachyolmia-amelogenesis imperfecta syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 11, 2023 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 25, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at