rs1489024588
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_052813.5(CARD9):c.1359C>T(p.Gly453=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000187 in 1,608,410 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. Synonymous variant affecting the same amino acid position (i.e. G453G) has been classified as Likely benign.
Frequency
Consequence
NM_052813.5 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 |
---|---|---|---|---|---|---|---|
CARD9 | NM_052813.5 | c.1359C>T | p.Gly453= | splice_region_variant, synonymous_variant | 11/13 | ENST00000371732.10 | |
LOC124902309 | XR_007061863.1 | n.84+1764G>A | intron_variant, non_coding_transcript_variant | ||||
CARD9 | NM_052814.4 | c.1359C>T | p.Gly453= | splice_region_variant, synonymous_variant | 11/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CARD9 | ENST00000371732.10 | c.1359C>T | p.Gly453= | splice_region_variant, synonymous_variant | 11/13 | 1 | NM_052813.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1456244Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 724692
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74334
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at