7-2906685-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP4_StrongBP6
The NM_032415.7(CARD11):c.3418G>A(p.Gly1140Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000737 in 1,613,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. G1140G) 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CARD11 | NM_032415.7 | c.3418G>A | p.Gly1140Ser | missense_variant | 25/25 | ENST00000396946.9 | |
CARD11 | NM_001324281.3 | c.3418G>A | p.Gly1140Ser | missense_variant | 26/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CARD11 | ENST00000396946.9 | c.3418G>A | p.Gly1140Ser | missense_variant | 25/25 | 1 | NM_032415.7 | P1 | |
CARD11 | ENST00000698637.1 | n.4528G>A | non_coding_transcript_exon_variant | 24/24 | |||||
CARD11 | ENST00000698652.1 | n.2374G>A | non_coding_transcript_exon_variant | 8/8 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152262Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251088Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135770
GnomAD4 exome AF: 0.0000773 AC: 113AN: 1461628Hom.: 0 Cov.: 30 AF XY: 0.0000743 AC XY: 54AN XY: 727138
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152262Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74382
ClinVar
Submissions by phenotype
CARD11-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 12, 2023 | The CARD11 c.3418G>A variant is predicted to result in the amino acid substitution p.Gly1140Ser. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0050% of alleles in individuals of East Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/7-2946319-C-T). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Severe combined immunodeficiency due to CARD11 deficiency;C4551967:BENTA disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at