rs35219727
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_005214.5(CTLA4):c.110-1260G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00139 in 152,324 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0014 ( 5 hom., cov: 32)
Consequence
CTLA4
NM_005214.5 intron
NM_005214.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.16
Genes affected
CTLA4 (HGNC:2505): (cytotoxic T-lymphocyte associated protein 4) This gene is a member of the immunoglobulin superfamily and encodes a protein which transmits an inhibitory signal to T cells. The protein contains a V domain, a transmembrane domain, and a cytoplasmic tail. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. The membrane-bound isoform functions as a homodimer interconnected by a disulfide bond, while the soluble isoform functions as a monomer. Mutations in this gene have been associated with insulin-dependent diabetes mellitus, Graves disease, Hashimoto thyroiditis, celiac disease, systemic lupus erythematosus, thyroid-associated orbitopathy, and other autoimmune diseases. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00139 (211/152324) while in subpopulation EAS AF= 0.0233 (121/5194). AF 95% confidence interval is 0.0199. There are 5 homozygotes in gnomad4. There are 108 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 211 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTLA4 | NM_005214.5 | c.110-1260G>A | intron_variant | ENST00000648405.2 | NP_005205.2 | |||
CTLA4 | NM_001037631.3 | c.110-1260G>A | intron_variant | NP_001032720.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CTLA4 | ENST00000648405.2 | c.110-1260G>A | intron_variant | NM_005214.5 | ENSP00000497102.1 |
Frequencies
GnomAD3 genomes AF: 0.00139 AC: 212AN: 152206Hom.: 5 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00139 AC: 211AN: 152324Hom.: 5 Cov.: 32 AF XY: 0.00145 AC XY: 108AN XY: 74486
GnomAD4 genome
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32
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108
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36
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at