16-31360000-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_000887.5(ITGAX):c.642C>T(p.Ser214Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,928 control chromosomes in the GnomAD database, with no homozygous occurrence. 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
Consequence
NM_000887.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITGAX | ENST00000268296.9 | c.642C>T | p.Ser214Ser | synonymous_variant | Exon 7 of 30 | 1 | NM_000887.5 | ENSP00000268296.5 | ||
ITGAX | ENST00000562522.2 | c.642C>T | p.Ser214Ser | synonymous_variant | Exon 7 of 31 | 1 | ENSP00000454623.1 | |||
ITGAX | ENST00000571644.1 | n.64C>T | non_coding_transcript_exon_variant | Exon 1 of 22 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251268Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135834
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461714Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 727180
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at