rs199705831
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_032415.7(CARD11):c.3019+6C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00421 in 1,591,864 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_032415.7 splice_region, intron
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 |
---|---|---|---|---|---|---|---|---|
CARD11 | NM_032415.7 | c.3019+6C>T | splice_region_variant, intron_variant | Intron 22 of 24 | ENST00000396946.9 | NP_115791.3 | ||
CARD11 | NM_001324281.3 | c.3019+6C>T | splice_region_variant, intron_variant | Intron 23 of 25 | NP_001311210.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CARD11 | ENST00000396946.9 | c.3019+6C>T | splice_region_variant, intron_variant | Intron 22 of 24 | 1 | NM_032415.7 | ENSP00000380150.4 | |||
CARD11 | ENST00000698637.1 | n.4129+6C>T | splice_region_variant, intron_variant | Intron 21 of 23 | ||||||
CARD11 | ENST00000698652.1 | n.1975+6C>T | splice_region_variant, intron_variant | Intron 5 of 7 |
Frequencies
GnomAD3 genomes AF: 0.00400 AC: 603AN: 150820Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00596 AC: 1408AN: 236438Hom.: 6 AF XY: 0.00510 AC XY: 658AN XY: 129088
GnomAD4 exome AF: 0.00423 AC: 6096AN: 1440926Hom.: 18 Cov.: 32 AF XY: 0.00409 AC XY: 2925AN XY: 715704
GnomAD4 genome AF: 0.00399 AC: 602AN: 150938Hom.: 4 Cov.: 32 AF XY: 0.00367 AC XY: 271AN XY: 73792
ClinVar
Submissions by phenotype
not specified Benign:1
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Severe combined immunodeficiency due to CARD11 deficiency;C4551967:BENTA disease Benign:1
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CARD11-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at