chr17-47283410-CTG-C
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000212.3(ITGB3):c.225_226delTG(p.Ala76ProfsTer10) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,888 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
ITGB3
NM_000212.3 frameshift
NM_000212.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 10.0
Publications
0 publications found
Genes affected
ITGB3 (HGNC:6156): (integrin subunit beta 3) The ITGB3 protein product is the integrin beta chain beta 3. Integrins are integral cell-surface proteins composed of an alpha chain and a beta chain. A given chain may combine with multiple partners resulting in different integrins. Integrin beta 3 is found along with the alpha IIb chain in platelets. Integrins are known to participate in cell adhesion as well as cell-surface mediated signalling. [provided by RefSeq, Jul 2008]
ENSG00000259753 (HGNC:):
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ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 18 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-47283410-CTG-C is Pathogenic according to our data. Variant chr17-47283410-CTG-C is described in ClinVar as Pathogenic. ClinVar VariationId is 1330313.Status of the report is reviewed_by_expert_panel, 3 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000212.3. 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 |
|---|---|---|---|---|---|---|---|---|---|
| ITGB3 | NM_000212.3 | MANE Select | c.225_226delTG | p.Ala76ProfsTer10 | frameshift | Exon 3 of 15 | NP_000203.2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ITGB3 | ENST00000559488.7 | TSL:1 MANE Select | c.225_226delTG | p.Ala76ProfsTer10 | frameshift | Exon 3 of 15 | ENSP00000452786.2 | P05106-1 | |
| ITGB3 | ENST00000571680.1 | TSL:1 | c.225_226delTG | p.Ala76ProfsTer10 | frameshift | Exon 3 of 9 | ENSP00000461626.1 | I3L4X8 | |
| ENSG00000259753 | ENST00000560629.1 | TSL:2 | n.189_190delTG | non_coding_transcript_exon | Exon 3 of 18 | ENSP00000456711.2 | H3BM21 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00000795 AC: 2AN: 251426 AF XY: 0.0000147 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
251426
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461888Hom.: 0 AF XY: 0.00000275 AC XY: 2AN XY: 727242 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
1461888
Hom.:
AF XY:
AC XY:
2
AN XY:
727242
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
2
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
53416
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1112010
Other (OTH)
AF:
AC:
0
AN:
60396
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
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0
1
1
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2
0.00
0.20
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Pathogenic
Revision:reviewed by expert panel
Pathogenic
VUS
Benign
Condition
1
-
-
Glanzmann thrombasthenia (1)
1
-
-
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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