2-32947621-A-ACCGCCGCCG
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3
The NM_206943.4(LTBP1):c.310_318dupCCGCCGCCG(p.Pro104_Pro106dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000129 in 1,327,092 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 0.000060 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00014 ( 0 hom. )
Consequence
LTBP1
NM_206943.4 conservative_inframe_insertion
NM_206943.4 conservative_inframe_insertion
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)
Genome browser will be placed here
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.310_318dupCCGCCGCCG | p.Pro104_Pro106dup | conservative_inframe_insertion | Exon 1 of 34 | NP_996826.3 | Q14766-1 | |
| LTBP1 | NM_001394905.1 | c.310_318dupCCGCCGCCG | p.Pro104_Pro106dup | conservative_inframe_insertion | 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.310_318dupCCGCCGCCG | p.Pro104_Pro106dup | conservative_inframe_insertion | Exon 1 of 34 | ENSP00000386043.2 | Q14766-1 | |
| LTBP1 | ENST00000929169.1 | c.310_318dupCCGCCGCCG | p.Pro104_Pro106dup | conservative_inframe_insertion | Exon 1 of 34 | ENSP00000599228.1 | |||
| LTBP1 | ENST00000954823.1 | c.310_318dupCCGCCGCCG | p.Pro104_Pro106dup | conservative_inframe_insertion | Exon 1 of 34 | ENSP00000624882.1 |
Frequencies
GnomAD3 genomes 0.0000598 AC: 9AN: 150406Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
9
AN:
150406
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.000138 AC: 162AN: 1176578Hom.: 0 Cov.: 33 AF XY: 0.000146 AC XY: 84AN XY: 573420 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
162
AN:
1176578
Hom.:
Cov.:
33
AF XY:
AC XY:
84
AN XY:
573420
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1
AN:
23190
American (AMR)
AF:
AC:
0
AN:
9590
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
15408
East Asian (EAS)
AF:
AC:
152
AN:
25158
South Asian (SAS)
AF:
AC:
0
AN:
45110
European-Finnish (FIN)
AF:
AC:
0
AN:
32302
Middle Eastern (MID)
AF:
AC:
0
AN:
3448
European-Non Finnish (NFE)
AF:
AC:
7
AN:
974964
Other (OTH)
AF:
AC:
2
AN:
47408
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.327
Heterozygous variant carriers
0
10
19
29
38
48
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
4
8
12
16
20
<30
30-35
35-40
40-45
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>80
Age
GnomAD4 genome 0.0000598 AC: 9AN: 150514Hom.: 0 Cov.: 32 AF XY: 0.0000816 AC XY: 6AN XY: 73524 show subpopulations
GnomAD4 genome
AF:
AC:
9
AN:
150514
Hom.:
Cov.:
32
AF XY:
AC XY:
6
AN XY:
73524
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41244
American (AMR)
AF:
AC:
0
AN:
15168
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3460
East Asian (EAS)
AF:
AC:
8
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
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.531
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
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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