rs2290447
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_206943.4(LTBP1):c.1202-57A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0364 in 1,360,332 control chromosomes in the GnomAD database, including 2,232 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.078 ( 1000 hom., cov: 32)
Exomes 𝑓: 0.031 ( 1232 hom. )
Consequence
LTBP1
NM_206943.4 intron
NM_206943.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0320
Genes affected
LTBP1 (HGNC:6714): (latent transforming growth factor beta binding protein 1) The protein encoded by this gene belongs to the family of latent TGF-beta binding proteins (LTBPs). The secretion and activation of TGF-betas is regulated by their association with latency-associated proteins and with latent TGF-beta binding proteins. The product of this gene targets latent complexes of transforming growth factor beta to the extracellular matrix, where the latent cytokine is subsequently activated by several different mechanisms. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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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=-0.97).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LTBP1 | NM_206943.4 | c.1202-57A>G | intron_variant | ENST00000404816.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LTBP1 | ENST00000404816.7 | c.1202-57A>G | intron_variant | 5 | NM_206943.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0781 AC: 11872AN: 152082Hom.: 986 Cov.: 32
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GnomAD4 exome AF: 0.0312 AC: 37660AN: 1208132Hom.: 1232 AF XY: 0.0296 AC XY: 17997AN XY: 608960
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GnomAD4 genome ? AF: 0.0783 AC: 11911AN: 152200Hom.: 1000 Cov.: 32 AF XY: 0.0750 AC XY: 5581AN XY: 74422
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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