6-31415134-A-T

Variant names:

• chr6-31415134-A-T
• rs1882
• NM_001177519.3:c.*152A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001177519.3(MICA):​c.*152A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000225 in 890,350 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 30)
  • Exomes 𝑓: 0.0000022 (0 hom.)
• Consequence: MICA NM_001177519.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294
• Publications: 33 publications found

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]

ENSG00000288587 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001177519.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICA	NM_001177519.3	MANE Select	c.*152A>T		3_prime_UTR	Exon 6 of 6	NP_001170990.1
	MICA	NM_001289152.2		c.*152A>T		3_prime_UTR	Exon 6 of 6	NP_001276081.1
	MICA	NM_001289153.2		c.*152A>T		3_prime_UTR	Exon 6 of 6	NP_001276082.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICA	ENST00000449934.7	TSL:1 MANE Select	c.*152A>T		3_prime_UTR	Exon 6 of 6	ENSP00000413079.1
	MICA	ENST00000892120.1		c.*152A>T		3_prime_UTR	Exon 5 of 5	ENSP00000562179.1
	MICA	ENST00000616296.4	TSL:5	c.*152A>T		3_prime_UTR	Exon 6 of 6	ENSP00000482382.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 0.00000225 AC: 2 AN: 890350 Hom.: 0 Cov.: 13 AF XY: 0.00000430 AC XY: 2 AN XY: 464678

African (AFR) AF: 0.00 AC: 0 AN: 20010

American (AMR) AF: 0.00 AC: 0 AN: 41864

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20450

East Asian (EAS) AF: 0.00 AC: 0 AN: 34316

South Asian (SAS) AF: 0.0000137 AC: 1 AN: 72910

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 49172

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4270

European-Non Finnish (NFE) AF: 0.00000164 AC: 1 AN: 608142

Other (OTH) AF: 0.00 AC: 0 AN: 39216

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.0
DANN	Benign	0.50
PhyloP100		-0.29
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1882; hg19: chr6-31382911;