rs1135314
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_052813.5(CARD9):c.*292T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 1,296,282 control chromosomes in the GnomAD database, including 69,305 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_052813.5 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CARD9 | NM_052813.5 | c.*292T>C | 3_prime_UTR_variant | Exon 13 of 13 | ENST00000371732.10 | NP_434700.2 | ||
CARD9 | NM_052814.4 | c.*115T>C | 3_prime_UTR_variant | Exon 13 of 13 | NP_434701.1 | |||
LOC124902309 | XR_007061863.1 | n.84+558A>G | intron_variant | Intron 1 of 1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CARD9 | ENST00000371732 | c.*292T>C | 3_prime_UTR_variant | Exon 13 of 13 | 1 | NM_052813.5 | ENSP00000360797.5 | |||
ENSG00000289701 | ENST00000696169.1 | n.*1531T>C | non_coding_transcript_exon_variant | Exon 12 of 13 | ENSP00000512460.1 | |||||
ENSG00000289701 | ENST00000696169.1 | n.*1531T>C | 3_prime_UTR_variant | Exon 12 of 13 | ENSP00000512460.1 |
Frequencies
GnomAD3 genomes AF: 0.308 AC: 46890AN: 152100Hom.: 7606 Cov.: 35
GnomAD3 exomes AF: 0.319 AC: 47626AN: 149294Hom.: 8577 AF XY: 0.309 AC XY: 24749AN XY: 80102
GnomAD4 exome AF: 0.322 AC: 367936AN: 1144066Hom.: 61685 Cov.: 16 AF XY: 0.318 AC XY: 183053AN XY: 575504
GnomAD4 genome AF: 0.308 AC: 46942AN: 152216Hom.: 7620 Cov.: 35 AF XY: 0.307 AC XY: 22838AN XY: 74440
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 75% of patients studied by a panel of primary immunodeficiencies. Number of patients: 66. Only high quality variants are reported. -
not provided Benign:1
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Predisposition to invasive fungal disease due to CARD9 deficiency Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at