rs1041457
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000211.5(ITGB2):c.500-170T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 710,714 control chromosomes in the GnomAD database, including 43,650 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.37 ( 11001 hom., cov: 34)
Exomes 𝑓: 0.33 ( 32649 hom. )
Consequence
ITGB2
NM_000211.5 intron
NM_000211.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.03
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BP6
?
Variant 21-44901903-A-G is Benign according to our data. Variant chr21-44901903-A-G is described in ClinVar as [Benign]. Clinvar id is 1276148.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGB2 | NM_000211.5 | c.500-170T>C | intron_variant | ENST00000652462.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGB2 | ENST00000652462.1 | c.500-170T>C | intron_variant | NM_000211.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.374 AC: 56887AN: 151938Hom.: 10991 Cov.: 34
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GnomAD4 exome AF: 0.332 AC: 185369AN: 558658Hom.: 32649 AF XY: 0.329 AC XY: 94834AN XY: 288070
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GnomAD4 genome ? AF: 0.374 AC: 56933AN: 152056Hom.: 11001 Cov.: 34 AF XY: 0.370 AC XY: 27522AN XY: 74318
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 12, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at