7-2906703-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_032415.7(CARD11):c.3400G>A(p.Val1134Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,461,642 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 Uncertain significance (★).
Frequency
Consequence
NM_032415.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CARD11 | NM_032415.7 | c.3400G>A | p.Val1134Ile | missense_variant | 25/25 | ENST00000396946.9 | NP_115791.3 | |
CARD11 | NM_001324281.3 | c.3400G>A | p.Val1134Ile | missense_variant | 26/26 | NP_001311210.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CARD11 | ENST00000396946.9 | c.3400G>A | p.Val1134Ile | missense_variant | 25/25 | 1 | NM_032415.7 | ENSP00000380150.4 | ||
CARD11 | ENST00000698637.1 | n.4510G>A | non_coding_transcript_exon_variant | 24/24 | ||||||
CARD11 | ENST00000698652.1 | n.2356G>A | non_coding_transcript_exon_variant | 8/8 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461642Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 727134
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Severe combined immunodeficiency due to CARD11 deficiency;C4551967:BENTA disease Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 02, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CARD11 protein function. ClinVar contains an entry for this variant (Variation ID: 661119). This variant has not been reported in the literature in individuals affected with CARD11-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 1134 of the CARD11 protein (p.Val1134Ile). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at