rs9266825
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001177519.3(MICA):c.*123C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 1,202,572 control chromosomes in the GnomAD database, including 44,966 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 0.32 ( 8322 hom., cov: 31)
Exomes 𝑓: 0.25 ( 36644 hom. )
Consequence
MICA
NM_001177519.3 3_prime_UTR
NM_001177519.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.170
Genes affected
MICA (HGNC:7090): (MHC class I polypeptide-related sequence A) This gene encodes the highly polymorphic major histocompatability complex class I chain-related protein A. The protein product is expressed on the cell surface, although unlike canonical class I molecules it does not seem to associate with beta-2-microglobulin. It is a ligand for the NKG2-D type II integral membrane protein receptor. The protein functions as a stress-induced antigen that is broadly recognized by intestinal epithelial gamma delta T cells. Variations in this gene have been associated with susceptibility to psoriasis 1 and psoriatic arthritis, and the shedding of MICA-related antibodies and ligands is involved in the progression from monoclonal gammopathy of undetermined significance to multiple myeloma. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2014]
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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=-0.93).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MICA | NM_001177519.3 | c.*123C>A | 3_prime_UTR_variant | 6/6 | ENST00000449934.7 | ||
MICA | NM_001289152.2 | c.*123C>A | 3_prime_UTR_variant | 6/6 | |||
MICA | NM_001289153.2 | c.*123C>A | 3_prime_UTR_variant | 6/6 | |||
MICA | NM_001289154.2 | c.*123C>A | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MICA | ENST00000449934.7 | c.*123C>A | 3_prime_UTR_variant | 6/6 | 1 | NM_001177519.3 | P1 | ||
MICA | ENST00000421350.1 | c.*123C>A | 3_prime_UTR_variant | 5/5 | 5 | ||||
MICA | ENST00000616296.4 | c.*123C>A | 3_prime_UTR_variant | 6/6 | 5 | ||||
MICA | ENST00000674069.1 | c.*123C>A | 3_prime_UTR_variant | 6/6 |
Frequencies
GnomAD3 genomes ? AF: 0.320 AC: 48388AN: 151400Hom.: 8304 Cov.: 31
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GnomAD3 exomes AF: 0.310 AC: 77028AN: 248426Hom.: 13293 AF XY: 0.305 AC XY: 41161AN XY: 134872
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GnomAD4 exome AF: 0.247 AC: 259741AN: 1051054Hom.: 36644 Cov.: 17 AF XY: 0.251 AC XY: 135269AN XY: 539760
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GnomAD4 genome ? AF: 0.320 AC: 48456AN: 151518Hom.: 8322 Cov.: 31 AF XY: 0.326 AC XY: 24170AN XY: 74030
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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