Variant 6-31412384-G-GCTGCTGCTGCTGCT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001177519.3(MICA):c.952_953insCTGCTGCTGCTGCT(p.Gly318AlafsTer73) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.00022 ( 1 hom., cov: 0)

Exomes 𝑓: 0.00020 ( 2 hom. )

Failed GnomAD Quality Control

Consequence

MICA
NM_001177519.3 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.641

Variant links:

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]

MICA links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
MICA	NM_001177519.3 linkuse as main transcript	c.952_953insCTGCTGCTGCTGCT	p.Gly318AlafsTer73	frameshift_variant	5/6	ENST00000449934.7	NP_001170990.1
MICA	NM_001289152.2 linkuse as main transcript	c.661_662insCTGCTGCTGCTGCT	p.Gly221AlafsTer73	frameshift_variant	5/6		NP_001276081.1
MICA	NM_001289153.2 linkuse as main transcript	c.661_662insCTGCTGCTGCTGCT	p.Gly221AlafsTer73	frameshift_variant	5/6		NP_001276082.1
MICA	NM_001289154.2 linkuse as main transcript	c.538_539insCTGCTGCTGCTGCT	p.Gly180AlafsTer73	frameshift_variant	5/6		NP_001276083.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
MICA	ENST00000449934.7 linkuse as main transcript	c.952_953insCTGCTGCTGCTGCT	p.Gly318AlafsTer73	frameshift_variant	5/6	1	NM_001177519.3	ENSP00000413079	P1
MICA	ENST00000421350.1 linkuse as main transcript	c.625_626insCTGCTGCTGCTGCT	p.Gly209AlafsTer73	frameshift_variant	4/5	5		ENSP00000402410
MICA	ENST00000616296.4 linkuse as main transcript	c.661_662insCTGCTGCTGCTGCT	p.Gly221AlafsTer73	frameshift_variant	5/6	5		ENSP00000482382
MICA	ENST00000674069.1 linkuse as main transcript	c.538_539insCTGCTGCTGCTGCT	p.Gly180AlafsTer73	frameshift_variant	5/6			ENSP00000501157

Frequencies

GnomAD3 genomes

AF:

0.000215

AC:

AN:

120862

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000264

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000806

Gnomad ASJ

AF:

0.000659

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000236

Gnomad OTH

AF:

0.000582

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000204

AC:

220

AN:

1078826

Hom.:

Cov.:

AF XY:

0.000200

AC XY:

107

AN XY:

534680

show subpopulations

Gnomad4 AFR exome

AF:

0.000364

Gnomad4 AMR exome

AF:

0.0000666

Gnomad4 ASJ exome

AF:

0.000918

Gnomad4 EAS exome

AF:

0.0000426

Gnomad4 SAS exome

AF:

0.0000455

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000211

Gnomad4 OTH exome

AF:

0.000175

GnomAD4 genome

AF:

0.000215

AC:

AN:

120862

Hom.:

Cov.:

AF XY:

0.000205

AC XY:

AN XY:

58666

show subpopulations

Gnomad4 AFR

AF:

0.000264

Gnomad4 AMR

AF:

0.0000806

Gnomad4 ASJ

AF:

0.000659

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000236

Gnomad4 OTH

AF:

0.000582

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over