rs9888879

chr16-31299051-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000632.4(ITGAM):c.1707+1097T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,066 control chromosomes in the GnomAD database, including 7,908 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 0.25 (7908 hom., cov: 31)
• Consequence: ITGAM NM_000632.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGAM	NM_000632.4	c.1707+1097T>C		intron_variant		ENST00000544665.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGAM	ENST00000544665.9	c.1707+1097T>C		intron_variant		1	NM_000632.4	P4
ITGAM	ENST00000567031.1	c.453+1397T>C		intron_variant		1
ITGAM	ENST00000648685.1	c.1710+1097T>C		intron_variant				A1

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38158 AN: 151946 Hom.: 7872 Cov.: 31

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.233

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.252 AC: 38247 AN: 152066 Hom.: 7908 Cov.: 31 AF XY: 0.248 AC XY: 18435 AN XY: 74356

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.0137

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.232

Alfa AF: 0.151 Hom.: 4089

Bravo AF: 0.265

Asia WGS AF: 0.132 AC: 460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.1
Dann	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9888879; hg19: chr16-31310372;