rs2230429
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000887.5(ITGAX):c.1550C>A(p.Pro517His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,016 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P517R) has been classified as Benign.
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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGAX | NM_000887.5 | c.1550C>A | p.Pro517His | missense_variant | 14/30 | ENST00000268296.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGAX | ENST00000268296.9 | c.1550C>A | p.Pro517His | missense_variant | 14/30 | 1 | NM_000887.5 | P4 | |
ITGAX | ENST00000562522.2 | c.1550C>A | p.Pro517His | missense_variant | 14/31 | 1 | A2 | ||
ITGAX | ENST00000571644.1 | n.1571C>A | non_coding_transcript_exon_variant | 7/22 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461016Hom.: 0 Cov.: 53 AF XY: 0.00000138 AC XY: 1AN XY: 726834
GnomAD4 genome ? Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at