chr16-31260106-G-GCAC
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_000632.4(ITGAM):c.28+14_28+15insCAC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0000064 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ITGAM
NM_000632.4 intron
NM_000632.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.423
Genes affected
ITGAM (HGNC:6149): (integrin subunit alpha M) This gene encodes the integrin alpha M chain. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. This I-domain containing alpha integrin combines with the beta 2 chain (ITGB2) to form a leukocyte-specific integrin referred to as macrophage receptor 1 ('Mac-1'), or inactivated-C3b (iC3b) receptor 3 ('CR3'). The alpha M beta 2 integrin is important in the adherence of neutrophils and monocytes to stimulated endothelium, and also in the phagocytosis of complement coated particles. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP6
?
Variant 16-31260106-G-GCAC is Benign according to our data. Variant chr16-31260106-G-GCAC is described in ClinVar as [Likely_benign]. Clinvar id is 1670129.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGAM | NM_000632.4 | c.28+14_28+15insCAC | intron_variant | ENST00000544665.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGAM | ENST00000544665.9 | c.28+14_28+15insCAC | intron_variant | 1 | NM_000632.4 | P4 | |||
ITGAM | ENST00000648685.1 | c.28+14_28+15insCAC | intron_variant | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 3AN: 151976Hom.: 0 Cov.: 30 FAILED QC
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GnomAD3 exomes AF: 0.0000543 AC: 10AN: 184234Hom.: 0 AF XY: 0.0000609 AC XY: 6AN XY: 98560
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000641 AC: 9AN: 1404338Hom.: 0 Cov.: 26 AF XY: 0.00000862 AC XY: 6AN XY: 695900
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000197 AC: 3AN: 151976Hom.: 0 Cov.: 30 AF XY: 0.0000269 AC XY: 2AN XY: 74226
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 27, 2022 | - - |
Computational scores
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Name
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at