rs61747615
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_ModerateBP6_ModerateBP7BS1
The NM_000211.5(ITGB2):c.1497G>A(p.Lys499=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000327 in 1,613,466 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0017 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00018 ( 0 hom. )
Consequence
ITGB2
NM_000211.5 synonymous
NM_000211.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.428
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 -7 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
Variant 21-44890138-C-T is Benign according to our data. Variant chr21-44890138-C-T is described in ClinVar as [Benign]. Clinvar id is 461471.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr21-44890138-C-T is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=0.428 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00173 (264/152278) while in subpopulation AFR AF= 0.00601 (250/41568). AF 95% confidence interval is 0.0054. There are 0 homozygotes in gnomad4. There are 119 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGB2 | NM_000211.5 | c.1497G>A | p.Lys499= | synonymous_variant | 12/16 | ENST00000652462.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGB2 | ENST00000652462.1 | c.1497G>A | p.Lys499= | synonymous_variant | 12/16 | NM_000211.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00174 AC: 265AN: 152160Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000442 AC: 111AN: 250928Hom.: 0 AF XY: 0.000324 AC XY: 44AN XY: 135792
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GnomAD4 exome AF: 0.000180 AC: 263AN: 1461188Hom.: 0 Cov.: 33 AF XY: 0.000168 AC XY: 122AN XY: 726914
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GnomAD4 genome ? AF: 0.00173 AC: 264AN: 152278Hom.: 0 Cov.: 33 AF XY: 0.00160 AC XY: 119AN XY: 74450
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Leukocyte adhesion deficiency 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
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