rs1063632
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001177519.3(MICA):c.261G>A(p.Arg87=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0629 in 1,604,506 control chromosomes in the GnomAD database, including 3,853 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 0.066 ( 437 hom., cov: 32)
Exomes 𝑓: 0.063 ( 3416 hom. )
Consequence
MICA
NM_001177519.3 synonymous
NM_001177519.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.149
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP7
?
Synonymous conserved (PhyloP=-0.149 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0786 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MICA | NM_001177519.3 | c.261G>A | p.Arg87= | synonymous_variant | 2/6 | ENST00000449934.7 | |
MICA | NM_001289154.2 | c.19G>A | p.Gly7Arg | missense_variant | 2/6 | ||
MICA | NM_001289152.2 | c.-31G>A | 5_prime_UTR_variant | 2/6 | |||
MICA | NM_001289153.2 | c.-31G>A | 5_prime_UTR_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MICA | ENST00000449934.7 | c.261G>A | p.Arg87= | synonymous_variant | 2/6 | 1 | NM_001177519.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0663 AC: 10074AN: 151852Hom.: 433 Cov.: 32
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GnomAD3 exomes AF: 0.0641 AC: 14801AN: 230786Hom.: 615 AF XY: 0.0643 AC XY: 8057AN XY: 125376
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GnomAD4 exome AF: 0.0626 AC: 90894AN: 1452536Hom.: 3416 Cov.: 37 AF XY: 0.0629 AC XY: 45433AN XY: 721940
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GnomAD4 genome ? AF: 0.0664 AC: 10092AN: 151970Hom.: 437 Cov.: 32 AF XY: 0.0668 AC XY: 4960AN XY: 74306
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at