chr7-2917323-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_032415.7(CARD11):c.2670G>A(p.Ser890=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000226 in 1,602,554 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CARD11 | NM_032415.7 | c.2670G>A | p.Ser890= | synonymous_variant | 20/25 | ENST00000396946.9 | |
CARD11 | NM_001324281.3 | c.2670G>A | p.Ser890= | synonymous_variant | 21/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CARD11 | ENST00000396946.9 | c.2670G>A | p.Ser890= | synonymous_variant | 20/25 | 1 | NM_032415.7 | P1 | |
CARD11 | ENST00000480332.1 | n.808G>A | non_coding_transcript_exon_variant | 4/4 | 5 | ||||
CARD11 | ENST00000698637.1 | n.3780G>A | non_coding_transcript_exon_variant | 19/24 | |||||
CARD11 | ENST00000698652.1 | n.1626G>A | non_coding_transcript_exon_variant | 3/8 |
Frequencies
GnomAD3 genomes AF: 0.000565 AC: 86AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000215 AC: 53AN: 246386Hom.: 1 AF XY: 0.000248 AC XY: 33AN XY: 133124
GnomAD4 exome AF: 0.000190 AC: 276AN: 1450226Hom.: 1 Cov.: 30 AF XY: 0.000170 AC XY: 122AN XY: 719350
GnomAD4 genome AF: 0.000565 AC: 86AN: 152328Hom.: 0 Cov.: 33 AF XY: 0.000537 AC XY: 40AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Feb 08, 2022 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | CARD11: BP4, BP7 - |
Severe combined immunodeficiency due to CARD11 deficiency;C4551967:BENTA disease Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at