rs10781496
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000371732.10(CARD9):c.1357+166T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 737,666 control chromosomes in the GnomAD database, including 67,295 homozygotes. 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
Genomes: 𝑓 0.39 ( 12121 hom., cov: 33)
Exomes 𝑓: 0.43 ( 55174 hom. )
Consequence
CARD9
ENST00000371732.10 intron
ENST00000371732.10 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.670
Genes affected
CARD9 (HGNC:16391): (caspase recruitment domain family member 9) The protein encoded by this gene is a member of the CARD protein family, which is defined by the presence of a characteristic caspase-associated recruitment domain (CARD). CARD is a protein interaction domain known to participate in activation or suppression of CARD containing members of the caspase family, and thus plays an important regulatory role in cell apoptosis. This protein was identified by its selective association with the CARD domain of BCL10, a postive regulator of apoptosis and NF-kappaB activation, and is thought to function as a molecular scaffold for the assembly of a BCL10 signaling complex that activates NF-kappaB. Several alternatively spliced transcript variants have been observed, but their full-length nature is not clearly defined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CARD9 | NM_052813.5 | c.1357+166T>C | intron_variant | ENST00000371732.10 | NP_434700.2 | |||
LOC124902309 | XR_007061863.1 | n.85-990A>G | intron_variant, non_coding_transcript_variant | |||||
CARD9 | NM_052814.4 | c.1357+166T>C | intron_variant | NP_434701.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CARD9 | ENST00000371732.10 | c.1357+166T>C | intron_variant | 1 | NM_052813.5 | ENSP00000360797 | P1 |
Frequencies
GnomAD3 genomes AF: 0.391 AC: 59464AN: 151984Hom.: 12100 Cov.: 33
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GnomAD4 exome AF: 0.429 AC: 251446AN: 585564Hom.: 55174 Cov.: 7 AF XY: 0.425 AC XY: 132917AN XY: 312906
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GnomAD4 genome AF: 0.391 AC: 59529AN: 152102Hom.: 12121 Cov.: 33 AF XY: 0.391 AC XY: 29097AN XY: 74350
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at