chr2-181498640-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000885.6(ITGA4):c.1558A>C(p.Ser520Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000000689 in 1,451,070 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S520N) has been classified as Uncertain significance.
Frequency
Consequence
NM_000885.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGA4 | NM_000885.6 | c.1558A>C | p.Ser520Arg | missense_variant | 15/28 | ENST00000397033.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGA4 | ENST00000397033.7 | c.1558A>C | p.Ser520Arg | missense_variant | 15/28 | 1 | NM_000885.6 | P1 | |
ITGA4 | ENST00000233573.6 | c.1558A>C | p.Ser520Arg | missense_variant | 15/16 | 1 | |||
ITGA4 | ENST00000476824.1 | n.69A>C | non_coding_transcript_exon_variant | 1/8 | 1 | ||||
ITGA4 | ENST00000490435.5 | n.360A>C | non_coding_transcript_exon_variant | 1/3 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1451070Hom.: 0 Cov.: 28 AF XY: 0.00000139 AC XY: 1AN XY: 721814
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2024 | The c.1558A>C (p.S520R) alteration is located in exon 15 (coding exon 15) of the ITGA4 gene. This alteration results from a A to C substitution at nucleotide position 1558, causing the serine (S) at amino acid position 520 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.