rs146545469
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_032415.7(CARD11):c.2670G>T(p.Ser890=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,450,228 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S890S) has been classified as Likely benign.
Frequency
Consequence
NM_032415.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CARD11 | NM_032415.7 | c.2670G>T | p.Ser890= | synonymous_variant | 20/25 | ENST00000396946.9 | |
CARD11 | NM_001324281.3 | c.2670G>T | p.Ser890= | synonymous_variant | 21/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CARD11 | ENST00000396946.9 | c.2670G>T | p.Ser890= | synonymous_variant | 20/25 | 1 | NM_032415.7 | P1 | |
CARD11 | ENST00000480332.1 | n.808G>T | non_coding_transcript_exon_variant | 4/4 | 5 | ||||
CARD11 | ENST00000698637.1 | n.3780G>T | non_coding_transcript_exon_variant | 19/24 | |||||
CARD11 | ENST00000698652.1 | n.1626G>T | non_coding_transcript_exon_variant | 3/8 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000406 AC: 1AN: 246386Hom.: 0 AF XY: 0.00000751 AC XY: 1AN XY: 133124
GnomAD4 exome AF: 6.90e-7 AC: 1AN: 1450228Hom.: 0 Cov.: 30 AF XY: 0.00000139 AC XY: 1AN XY: 719352
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Severe combined immunodeficiency due to CARD11 deficiency;C4551967:BENTA disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 22, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at