rs1136470
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_002414.5(CD99):āc.363C>Gā(p.Ala121=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000374 in 1,603,160 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002414.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD99 | NM_002414.5 | c.363C>G | p.Ala121= | splice_region_variant, synonymous_variant | 8/10 | ENST00000381192.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD99 | ENST00000381192.10 | c.363C>G | p.Ala121= | splice_region_variant, synonymous_variant | 8/10 | 1 | NM_002414.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151982Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74226
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250760Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135510
GnomAD4 exome AF: 0.00000345 AC: 5AN: 1451178Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 722194
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151982Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74226
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at