chr6-31412380-TGCTG-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001177519.3(MICA):c.953_956del(p.Gly318AlafsTer67) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 1,527,462 control chromosomes in the GnomAD database, including 9,654 homozygotes. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.15 ( 946 hom., cov: 20)
Exomes 𝑓: 0.11 ( 8708 hom. )
Consequence
MICA
NM_001177519.3 frameshift
NM_001177519.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.131
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 -10 ACMG points.
BP6
?
Variant 6-31412380-TGCTG-T is Benign according to our data. Variant chr6-31412380-TGCTG-T is described in ClinVar as [Benign]. Clinvar id is 403086.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MICA | NM_001177519.3 | c.953_956del | p.Gly318AlafsTer67 | frameshift_variant | 5/6 | ENST00000449934.7 | |
MICA | NM_001289152.2 | c.662_665del | p.Gly221AlafsTer67 | frameshift_variant | 5/6 | ||
MICA | NM_001289153.2 | c.662_665del | p.Gly221AlafsTer67 | frameshift_variant | 5/6 | ||
MICA | NM_001289154.2 | c.539_542del | p.Gly180AlafsTer67 | frameshift_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MICA | ENST00000449934.7 | c.953_956del | p.Gly318AlafsTer67 | frameshift_variant | 5/6 | 1 | NM_001177519.3 | P1 | |
MICA | ENST00000421350.1 | c.626_629del | p.Gly209AlafsTer67 | frameshift_variant | 4/5 | 5 | |||
MICA | ENST00000616296.4 | c.662_665del | p.Gly221AlafsTer67 | frameshift_variant | 5/6 | 5 | |||
MICA | ENST00000674069.1 | c.539_542del | p.Gly180AlafsTer67 | frameshift_variant | 5/6 |
Frequencies
GnomAD3 genomes ? AF: 0.152 AC: 15660AN: 102830Hom.: 939 Cov.: 20
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GnomAD3 exomes AF: 0.158 AC: 17598AN: 111472Hom.: 1176 AF XY: 0.156 AC XY: 9334AN XY: 59832
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GnomAD4 exome AF: 0.106 AC: 151295AN: 1424570Hom.: 8708 AF XY: 0.106 AC XY: 74757AN XY: 705794
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GnomAD4 genome ? AF: 0.152 AC: 15683AN: 102892Hom.: 946 Cov.: 20 AF XY: 0.157 AC XY: 7771AN XY: 49540
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 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: Frequency in ESP (all): 2994/11918=25.12% - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at