19-40598907-AATC-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The ENST00000308370.11(LTBP4):c.147-288_147-286del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00543 in 152,216 control chromosomes in the GnomAD database, including 15 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0054 ( 15 hom., cov: 33)
Consequence
LTBP4
ENST00000308370.11 intron
ENST00000308370.11 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.975
Genes affected
LTBP4 (HGNC:6717): (latent transforming growth factor beta binding protein 4) The protein encoded by this gene binds transforming growth factor beta (TGFB) as it is secreted and targeted to the extracellular matrix. TGFB is biologically latent after secretion and insertion into the extracellular matrix, and sheds TGFB and other proteins upon activation. Defects in this gene may be a cause of cutis laxa and severe pulmonary, gastrointestinal, and urinary abnormalities. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 19-40598907-AATC-A is Benign according to our data. Variant chr19-40598907-AATC-A is described in ClinVar as [Likely_benign]. Clinvar id is 1219386.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00543 (827/152216) while in subpopulation AFR AF= 0.0177 (736/41522). AF 95% confidence interval is 0.0167. There are 15 homozygotes in gnomad4. There are 439 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 15 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LTBP4 | NM_001042544.1 | c.147-288_147-286del | intron_variant | NP_001036009.1 | ||||
LTBP4 | NM_003573.2 | c.17-288_17-286del | intron_variant | NP_003564.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LTBP4 | ENST00000204005.13 | c.17-288_17-286del | intron_variant | 1 | ENSP00000204005 | A2 | ||||
LTBP4 | ENST00000308370.11 | c.147-288_147-286del | intron_variant | 1 | ENSP00000311905 | A2 | ||||
LTBP4 | ENST00000594537.2 | c.94+287_95-286del | intron_variant, NMD_transcript_variant | 5 | ENSP00000480629 |
Frequencies
GnomAD3 genomes AF: 0.00543 AC: 826AN: 152098Hom.: 15 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00543 AC: 827AN: 152216Hom.: 15 Cov.: 33 AF XY: 0.00590 AC XY: 439AN XY: 74414
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 21, 2020 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at