rs142381225
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000211.5(ITGB2):c.807C>T(p.Phe269=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000427 in 1,614,062 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0022 ( 3 hom., cov: 33)
Exomes 𝑓: 0.00024 ( 2 hom. )
Consequence
ITGB2
NM_000211.5 synonymous
NM_000211.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.163
Genes affected
ITGB2 (HGNC:6155): (integrin subunit beta 2) This gene encodes an integrin beta chain, which combines with multiple different alpha chains to form different integrin heterodimers. Integrins are integral cell-surface proteins that participate in cell adhesion as well as cell-surface mediated signalling. The encoded protein plays an important role in immune response and defects in this gene cause leukocyte adhesion deficiency. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 21-44900410-G-A is Benign according to our data. Variant chr21-44900410-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 530691.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44900410-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.163 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00222 (338/152306) while in subpopulation AFR AF= 0.00724 (301/41576). AF 95% confidence interval is 0.00657. There are 3 homozygotes in gnomad4. There are 181 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGB2 | NM_000211.5 | c.807C>T | p.Phe269= | synonymous_variant | 7/16 | ENST00000652462.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGB2 | ENST00000652462.1 | c.807C>T | p.Phe269= | synonymous_variant | 7/16 | NM_000211.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00221 AC: 337AN: 152188Hom.: 3 Cov.: 33
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GnomAD3 exomes AF: 0.000545 AC: 137AN: 251284Hom.: 0 AF XY: 0.000486 AC XY: 66AN XY: 135868
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GnomAD4 exome AF: 0.000240 AC: 351AN: 1461756Hom.: 2 Cov.: 33 AF XY: 0.000204 AC XY: 148AN XY: 727162
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GnomAD4 genome ? AF: 0.00222 AC: 338AN: 152306Hom.: 3 Cov.: 33 AF XY: 0.00243 AC XY: 181AN XY: 74464
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Leukocyte adhesion deficiency 1 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
ITGB2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 10, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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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