16-31268215-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000632.4(ITGAM):​c.427+2068T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,016 control chromosomes in the GnomAD database, including 35,354 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 0.68 ( 35354 hom., cov: 31)

Consequence

ITGAM
NM_000632.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0710
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ITGAMNM_000632.4 linkuse as main transcriptc.427+2068T>C intron_variant ENST00000544665.9 NP_000623.2 P11215-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ITGAMENST00000544665.9 linkuse as main transcriptc.427+2068T>C intron_variant 1 NM_000632.4 ENSP00000441691.3 P11215-1
ITGAMENST00000648685.1 linkuse as main transcriptc.427+2068T>C intron_variant ENSP00000496959.1 P11215-2

Frequencies

GnomAD3 genomes
AF:
0.679
AC:
103083
AN:
151898
Hom.:
35321
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.749
Gnomad AMI
AF:
0.623
Gnomad AMR
AF:
0.593
Gnomad ASJ
AF:
0.803
Gnomad EAS
AF:
0.707
Gnomad SAS
AF:
0.464
Gnomad FIN
AF:
0.595
Gnomad MID
AF:
0.854
Gnomad NFE
AF:
0.674
Gnomad OTH
AF:
0.711
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.679
AC:
103161
AN:
152016
Hom.:
35354
Cov.:
31
AF XY:
0.672
AC XY:
49945
AN XY:
74312
show subpopulations
Gnomad4 AFR
AF:
0.749
Gnomad4 AMR
AF:
0.592
Gnomad4 ASJ
AF:
0.803
Gnomad4 EAS
AF:
0.708
Gnomad4 SAS
AF:
0.465
Gnomad4 FIN
AF:
0.595
Gnomad4 NFE
AF:
0.674
Gnomad4 OTH
AF:
0.709
Alfa
AF:
0.679
Hom.:
46849
Bravo
AF:
0.686
Asia WGS
AF:
0.581
AC:
2019
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
2.7
DANN
Benign
0.56

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs8048583; hg19: chr16-31279536; API