rs12928810
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000544665.9(ITGAM):c.1707+2440G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,108 control chromosomes in the GnomAD database, including 3,065 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.18 ( 3065 hom., cov: 32)
Consequence
ITGAM
ENST00000544665.9 intron
ENST00000544665.9 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.08
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 Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITGAM | NM_000632.4 | c.1707+2440G>A | intron_variant | ENST00000544665.9 | NP_000623.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITGAM | ENST00000544665.9 | c.1707+2440G>A | intron_variant | 1 | NM_000632.4 | ENSP00000441691 | P4 | |||
ITGAM | ENST00000567031.1 | c.453+2740G>A | intron_variant | 1 | ENSP00000454568 | |||||
ITGAM | ENST00000648685.1 | c.1710+2440G>A | intron_variant | ENSP00000496959 | A1 |
Frequencies
GnomAD3 genomes AF: 0.178 AC: 27076AN: 151990Hom.: 3047 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.178 AC: 27139AN: 152108Hom.: 3065 Cov.: 32 AF XY: 0.177 AC XY: 13196AN XY: 74354
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414
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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