chr16-31301932-C-T

Position:

• chr16-31301932-C-T

Variant summary

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

The ENST00000544665.9(ITGAM):​c.1707+3978C>T 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 151,968 control chromosomes in the GnomAD database, including 7,873 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 (7873 hom., cov: 32)
• Consequence: ITGAM ENST00000544665.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGAM	NM_000632.4	c.1707+3978C>T		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+3978C>T		intron_variant		1	NM_000632.4	ENSP00000441691	P4
ITGAM	ENST00000567031.1	c.453+4278C>T		intron_variant		1		ENSP00000454568
ITGAM	ENST00000648685.1	c.1710+3978C>T		intron_variant				ENSP00000496959	A1

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38134 AN: 151850 Hom.: 7837 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0143

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.123

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: 38223 AN: 151968 Hom.: 7873 Cov.: 32 AF XY: 0.248 AC XY: 18436 AN XY: 74262

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.232

Alfa AF: 0.145 Hom.: 4646

Bravo AF: 0.265

Asia WGS AF: 0.132 AC: 458 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.0
DANN	Benign	0.30

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: rs9888739; hg19: chr16-31313253;