16-31359826-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000887.5(ITGAX):c.557C>A(p.Thr186Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000805 in 1,614,068 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000887.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITGAX | ENST00000268296.9 | c.557C>A | p.Thr186Asn | missense_variant | Exon 6 of 30 | 1 | NM_000887.5 | ENSP00000268296.5 | ||
ITGAX | ENST00000562522.2 | c.557C>A | p.Thr186Asn | missense_variant | Exon 6 of 31 | 1 | ENSP00000454623.1 | |||
ITGAX | ENST00000571644.1 | n.-111C>A | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251366Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135868
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461846Hom.: 0 Cov.: 30 AF XY: 0.00000825 AC XY: 6AN XY: 727216
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.557C>A (p.T186N) alteration is located in exon 6 (coding exon 6) of the ITGAX gene. This alteration results from a C to A substitution at nucleotide position 557, causing the threonine (T) at amino acid position 186 to be replaced by an asparagine (N). 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