rs155103
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000885.6(ITGA4):c.1153+24A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 1,563,114 control chromosomes in the GnomAD database, including 457,531 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 0.76 ( 43632 hom., cov: 32)
Exomes 𝑓: 0.76 ( 413899 hom. )
Consequence
ITGA4
NM_000885.6 intron
NM_000885.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.139
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGA4 | NM_000885.6 | c.1153+24A>G | intron_variant | ENST00000397033.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGA4 | ENST00000397033.7 | c.1153+24A>G | intron_variant | 1 | NM_000885.6 | P1 | |||
ITGA4 | ENST00000233573.6 | c.1153+24A>G | intron_variant | 1 | |||||
ITGA4 | ENST00000465522.5 | n.1428A>G | non_coding_transcript_exon_variant | 10/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.755 AC: 114758AN: 151990Hom.: 43596 Cov.: 32
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GnomAD3 exomes AF: 0.749 AC: 157581AN: 210274Hom.: 59483 AF XY: 0.745 AC XY: 85942AN XY: 115334
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GnomAD4 exome AF: 0.764 AC: 1078495AN: 1411006Hom.: 413899 Cov.: 34 AF XY: 0.761 AC XY: 531950AN XY: 699410
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GnomAD4 genome ? AF: 0.755 AC: 114846AN: 152108Hom.: 43632 Cov.: 32 AF XY: 0.751 AC XY: 55846AN XY: 74338
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at