chr2-32947621-ACCGCCG-A
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3
The NM_206943.4(LTBP1):c.313_318delCCGCCG(p.Pro105_Pro106del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000264 in 1,327,078 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000028 ( 0 hom. )
Consequence
LTBP1
NM_206943.4 conservative_inframe_deletion
NM_206943.4 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.14
Publications
0 publications found
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]
LTBP1 Gene-Disease associations (from GenCC):
- cutis laxa, autosomal recessive, type 2EInheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_206943.4
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_206943.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| LTBP1 | NM_206943.4 | MANE Select | c.313_318delCCGCCG | p.Pro105_Pro106del | conservative_inframe_deletion | Exon 1 of 34 | NP_996826.3 | Q14766-1 | |
| LTBP1 | NM_001394905.1 | c.313_318delCCGCCG | p.Pro105_Pro106del | conservative_inframe_deletion | Exon 1 of 34 | NP_001381834.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| LTBP1 | ENST00000404816.7 | TSL:5 MANE Select | c.313_318delCCGCCG | p.Pro105_Pro106del | conservative_inframe_deletion | Exon 1 of 34 | ENSP00000386043.2 | Q14766-1 | |
| LTBP1 | ENST00000929169.1 | c.313_318delCCGCCG | p.Pro105_Pro106del | conservative_inframe_deletion | Exon 1 of 34 | ENSP00000599228.1 | |||
| LTBP1 | ENST00000954823.1 | c.313_318delCCGCCG | p.Pro105_Pro106del | conservative_inframe_deletion | Exon 1 of 34 | ENSP00000624882.1 |
Frequencies
GnomAD3 genomes 0.0000133 AC: 2AN: 150406Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
150406
Hom.:
Cov.:
32
Gnomad AFR
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GnomAD2 exomes AF: 0.00 AC: 0AN: 8816 AF XY: 0.00
GnomAD2 exomes
AF:
AC:
0
AN:
8816
AF XY:
Gnomad AFR exome
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GnomAD4 exome AF: 0.0000280 AC: 33AN: 1176564Hom.: 0 AF XY: 0.0000331 AC XY: 19AN XY: 573408 show subpopulations
GnomAD4 exome
AF:
AC:
33
AN:
1176564
Hom.:
AF XY:
AC XY:
19
AN XY:
573408
show subpopulations
African (AFR)
AF:
AC:
0
AN:
23190
American (AMR)
AF:
AC:
1
AN:
9590
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
15408
East Asian (EAS)
AF:
AC:
2
AN:
25208
South Asian (SAS)
AF:
AC:
9
AN:
45088
European-Finnish (FIN)
AF:
AC:
0
AN:
32302
Middle Eastern (MID)
AF:
AC:
0
AN:
3448
European-Non Finnish (NFE)
AF:
AC:
18
AN:
974922
Other (OTH)
AF:
AC:
3
AN:
47408
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
2
3
5
6
8
0.00
0.20
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0.60
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome 0.0000133 AC: 2AN: 150514Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73524 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
2
AN:
150514
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
73524
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
41244
American (AMR)
AF:
AC:
1
AN:
15168
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3460
East Asian (EAS)
AF:
AC:
0
AN:
5074
South Asian (SAS)
AF:
AC:
0
AN:
4810
European-Finnish (FIN)
AF:
AC:
0
AN:
10100
Middle Eastern (MID)
AF:
AC:
0
AN:
290
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67366
Other (OTH)
AF:
AC:
0
AN:
2090
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.00000000770867), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.400
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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