9-136364350-GTCC-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_052813.5(CARD9):c.1560_1562delGGA(p.Glu520del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000363 in 1,570,322 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_052813.5 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CARD9 | NM_052813.5 | c.1560_1562delGGA | p.Glu520del | disruptive_inframe_deletion | Exon 13 of 13 | ENST00000371732.10 | NP_434700.2 | |
CARD9 | NM_052814.4 | c.1442-191_1442-189delGGA | intron_variant | Intron 12 of 12 | NP_434701.1 | |||
LOC124902309 | XR_007061863.1 | n.84+905_84+907delTCC | intron_variant | Intron 1 of 1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CARD9 | ENST00000371732.10 | c.1560_1562delGGA | p.Glu520del | disruptive_inframe_deletion | Exon 13 of 13 | 1 | NM_052813.5 | ENSP00000360797.5 | ||
ENSG00000289701 | ENST00000696169.1 | n.*1188_*1190delGGA | non_coding_transcript_exon_variant | Exon 12 of 13 | ENSP00000512460.1 | |||||
ENSG00000289701 | ENST00000696169.1 | n.*1188_*1190delGGA | 3_prime_UTR_variant | Exon 12 of 13 | ENSP00000512460.1 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152230Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.0000271 AC: 5AN: 184224Hom.: 0 AF XY: 0.0000202 AC XY: 2AN XY: 98894
GnomAD4 exome AF: 0.0000219 AC: 31AN: 1418092Hom.: 0 AF XY: 0.0000143 AC XY: 10AN XY: 701696
GnomAD4 genome AF: 0.000171 AC: 26AN: 152230Hom.: 1 Cov.: 34 AF XY: 0.000215 AC XY: 16AN XY: 74368
ClinVar
Submissions by phenotype
Predisposition to invasive fungal disease due to CARD9 deficiency Uncertain:1
This variant, c.1560_1562del, results in the deletion of 1 amino acid(s) of the CARD9 protein (p.Glu520del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs756632228, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with CARD9-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at