chr7-2930050-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP2BP4_StrongBP6BS1
The NM_032415.7(CARD11):c.1595C>T(p.Thr532Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000232 in 1,613,906 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. T532T) has been classified as Likely benign.
Frequency
Consequence
NM_032415.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CARD11 | NM_032415.7 | c.1595C>T | p.Thr532Met | missense_variant | 12/25 | ENST00000396946.9 | |
CARD11 | NM_001324281.3 | c.1595C>T | p.Thr532Met | missense_variant | 13/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CARD11 | ENST00000396946.9 | c.1595C>T | p.Thr532Met | missense_variant | 12/25 | 1 | NM_032415.7 | P1 | |
CARD11 | ENST00000355508.3 | c.11C>T | p.Thr4Met | missense_variant | 1/7 | 3 | |||
CARD11 | ENST00000698637.1 | n.1921C>T | non_coding_transcript_exon_variant | 12/24 |
Frequencies
GnomAD3 genomes AF: 0.000269 AC: 41AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000406 AC: 102AN: 251204Hom.: 0 AF XY: 0.000361 AC XY: 49AN XY: 135784
GnomAD4 exome AF: 0.000228 AC: 333AN: 1461600Hom.: 0 Cov.: 32 AF XY: 0.000217 AC XY: 158AN XY: 727122
GnomAD4 genome AF: 0.000269 AC: 41AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74472
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Blueprint Genetics | Jun 27, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | CARD11: PP2, BP4, BS1 - |
not specified Benign:1Other:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 07, 2021 | - - |
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Severe combined immunodeficiency due to CARD11 deficiency;C4551967:BENTA disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at