rs775400791
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 1P and 3B. PP2BP4BP6_Moderate
The NM_032415.7(CARD11):c.2801C>T(p.Ser934Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000248 in 1,613,996 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict 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. S934S) has been classified as Likely benign.
Frequency
Consequence
NM_032415.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CARD11 | NM_032415.7 | c.2801C>T | p.Ser934Leu | missense_variant | 21/25 | ENST00000396946.9 | |
CARD11 | NM_001324281.3 | c.2801C>T | p.Ser934Leu | missense_variant | 22/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CARD11 | ENST00000396946.9 | c.2801C>T | p.Ser934Leu | missense_variant | 21/25 | 1 | NM_032415.7 | P1 | |
CARD11 | ENST00000698637.1 | n.3911C>T | non_coding_transcript_exon_variant | 20/24 | |||||
CARD11 | ENST00000698652.1 | n.1757C>T | non_coding_transcript_exon_variant | 4/8 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251014Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135826
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461764Hom.: 0 Cov.: 32 AF XY: 0.0000303 AC XY: 22AN XY: 727180
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74374
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 | Oct 25, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at