2-181537617-A-G

Variant summary

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

The NM_000885.6(ITGA4):c.*2090A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00246 in 430,388 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.0024 (10 hom., cov: 32)
  • Exomes 𝑓: 0.0025 (15 hom.)
• Consequence: ITGA4 NM_000885.6 3_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.386

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]

CERKL (HGNC:21699): (ceramide kinase like) This gene was initially identified as a locus (RP26) associated with an autosomal recessive form of retinitis pigmentosa (arRP) disease. This gene encodes a protein with ceramide kinase-like domains, however, the protein does not phosphorylate ceramide and its target substrate is currently unknown. This protein may be a negative regulator of apoptosis in photoreceptor cells. Mutations in this gene cause a form of retinitis pigmentosa characterized by autosomal recessive cone and rod dystrophy (arCRD). Alternative splicing of this gene results in multiple transcript variants encoding different isoforms and non-coding transcripts.[provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA4	NM_000885.6	c.*2090A>G		3_prime_UTR_variant	28/28	ENST00000397033.7
CERKL	NM_201548.5	c.*567T>C		3_prime_UTR_variant	13/13	ENST00000410087.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA4	ENST00000397033.7	c.*2090A>G		3_prime_UTR_variant	28/28	1	NM_000885.6	P1
CERKL	ENST00000410087.8	c.*567T>C		3_prime_UTR_variant	13/13	1	NM_201548.5	P1
CERKL	ENST00000409440.7	c.*567T>C		3_prime_UTR_variant	13/13	2
CERKL	ENST00000684145.1	c.*567T>C		3_prime_UTR_variant	12/12

Frequencies

GnomAD3 genomes AF: 0.00241 AC: 366 AN: 152106 Hom.: 10 Cov.: 32

Gnomad AFR AF: 0.000314

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000328

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.0554

Gnomad SAS AF: 0.000828

Gnomad FIN AF: 0.000471

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000706

Gnomad OTH AF: 0.000957

GnomAD3 exomes AF: 0.00548 AC: 584 AN: 106620 Hom.: 13 AF XY: 0.00483 AC XY: 282 AN XY: 58372

Gnomad AFR exome AF: 0.000351

Gnomad AMR exome AF: 0.000105

Gnomad ASJ exome AF: 0.00120

Gnomad EAS exome AF: 0.0559

Gnomad SAS exome AF: 0.00118

Gnomad FIN exome AF: 0.000922

Gnomad NFE exome AF: 0.000581

Gnomad OTH exome AF: 0.00212

GnomAD4 exome AF: 0.00249 AC: 694 AN: 278164 Hom.: 15 Cov.: 0 AF XY: 0.00229 AC XY: 364 AN XY: 158840

Gnomad4 AFR exome AF: 0.000425

Gnomad4 AMR exome AF: 0.0000931

Gnomad4 ASJ exome AF: 0.000831

Gnomad4 EAS exome AF: 0.0518

Gnomad4 SAS exome AF: 0.00107

Gnomad4 FIN exome AF: 0.000259

Gnomad4 NFE exome AF: 0.000748

Gnomad4 OTH exome AF: 0.00278

GnomAD4 genome AF: 0.00240 AC: 366 AN: 152224 Hom.: 10 Cov.: 32 AF XY: 0.00271 AC XY: 202 AN XY: 74448

Gnomad4 AFR AF: 0.000313

Gnomad4 AMR AF: 0.000327

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.0556

Gnomad4 SAS AF: 0.000829

Gnomad4 FIN AF: 0.000471

Gnomad4 NFE AF: 0.000706

Gnomad4 OTH AF: 0.000947

Alfa AF: 0.00110 Hom.: 0

Bravo AF: 0.00294

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Retinitis pigmentosa Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.33
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490690; hg19: chr2-182402344;