rs231775
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005214.5(CTLA4):āc.49A>Gā(p.Thr17Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 1,613,082 control chromosomes in the GnomAD database, including 128,827 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T17I) has been classified as Uncertain significance.
Frequency
Consequence
NM_005214.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTLA4 | NM_005214.5 | c.49A>G | p.Thr17Ala | missense_variant | 1/4 | ENST00000648405.2 | |
CTLA4 | NM_001037631.3 | c.49A>G | p.Thr17Ala | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTLA4 | ENST00000648405.2 | c.49A>G | p.Thr17Ala | missense_variant | 1/4 | NM_005214.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.400 AC: 60714AN: 151936Hom.: 12575 Cov.: 32
GnomAD3 exomes AF: 0.415 AC: 104287AN: 251236Hom.: 22926 AF XY: 0.406 AC XY: 55192AN XY: 135776
GnomAD4 exome AF: 0.393 AC: 573983AN: 1461028Hom.: 116235 Cov.: 39 AF XY: 0.390 AC XY: 283226AN XY: 726866
GnomAD4 genome AF: 0.400 AC: 60776AN: 152054Hom.: 12592 Cov.: 32 AF XY: 0.407 AC XY: 30216AN XY: 74324
ClinVar
Submissions by phenotype
not provided Benign:1Other:1
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | This variant is associated with the following publications: (PMID: 19737153, 19037649, 22497911, 20920330, 21387262, 18757416, 23830732, 21503616, 21612409, 22011251, 19884265, 20145677, 11426323, 21453059, 22905924, 20538028, 23246583, 19922464, 11976786, 12417883, 22699762, 21346773, 21629267, 20940051, 9259273, 24517008, 28220572) - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF - |
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Hashimoto thyroiditis, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Apr 01, 2005 | - - |
TYPE 1 DIABETES MELLITUS 12, SUSCEPTIBILITY TO Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Apr 01, 2005 | - - |
THYROID-ASSOCIATED ORBITOPATHY, SUSCEPTIBILITY TO Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Apr 01, 2005 | - - |
Systemic lupus erythematosus, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Apr 01, 2005 | - - |
Celiac disease, susceptibility to, 3 Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Apr 01, 2005 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at