NM_000885.6:c.1922+1039G>A

Variant names:

• chr2-181512814-G-A
• rs3770112
• NM_000885.6:c.1922+1039G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000885.6(ITGA4):​c.1922+1039G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,976 control chromosomes in the GnomAD database, including 4,839 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 0.23 (4839 hom., cov: 32)
• Consequence: ITGA4 NM_000885.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398
• Publications: 7 publications found

Genes affected

ITGA4 (HGNC:6140): (integrin subunit alpha 4) The gene encodes a member of the integrin alpha chain family of proteins. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain that function in cell surface adhesion and signaling. The encoded preproprotein is proteolytically processed to generate light and heavy chains that comprise the alpha 4 subunit. This subunit associates with a beta 1 or beta 7 subunit to form an integrin that may play a role in cell motility and migration. This integrin is a therapeutic target for the treatment of multiple sclerosis, Crohn's disease and inflammatory bowel disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGA4	NM_000885.6	c.1922+1039G>A		intron_variant	Intron 17 of 27	ENST00000397033.7	NP_000876.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA4	ENST00000397033.7	c.1922+1039G>A		intron_variant	Intron 17 of 27	1	NM_000885.6	ENSP00000380227.2
ITGA4	ENST00000476824.1	n.433+1039G>A		intron_variant	Intron 3 of 7	1

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35386 AN: 151860 Hom.: 4837 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.233 AC: 35401 AN: 151976 Hom.: 4839 Cov.: 32 AF XY: 0.226 AC XY: 16806 AN XY: 74294

African (AFR) AF: 0.118 AC: 4911 AN: 41480

American (AMR) AF: 0.201 AC: 3060 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1083 AN: 3470

East Asian (EAS) AF: 0.148 AC: 761 AN: 5158

South Asian (SAS) AF: 0.104 AC: 499 AN: 4820

European-Finnish (FIN) AF: 0.275 AC: 2914 AN: 10586

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.310 AC: 21058 AN: 67898

Other (OTH) AF: 0.255 AC: 538 AN: 2110

Alfa AF: 0.261 Hom.: 3321

Bravo AF: 0.228

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.57
PhyloP100		0.40
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3770112; hg19: chr2-182377541;