chr6-31498042-C-A

Variant names:

• chr6-31498042-C-A
• rs3828914
• NM_001289160.2:c.-27+3047C>A

Variant summary

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

The NM_001289160.2(MICB):​c.-27+3047C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MICB NM_001289160.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• Publications: 35 publications found

Genes affected

MICB (HGNC:7091): (MHC class I polypeptide-related sequence B) This gene encodes a heavily glycosylated protein which is a ligand for the NKG2D type II receptor. Binding of the ligand activates the cytolytic response of natural killer (NK) cells, CD8 alphabeta T cells, and gammadelta T cells which express the receptor. This protein is stress-induced and is similar to MHC class I molecules; however, it does not associate with beta-2-microglobulin or bind peptides. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

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=-0.79).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001289160.2. 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
	MICB	NM_001289160.2		c.-27+3047C>A		intron	N/A	NP_001276089.1
	MICB	NM_005931.5	MANE Select	c.-152C>A		upstream_gene	N/A	NP_005922.2
	MICB	NM_001289161.2		c.-152C>A		upstream_gene	N/A	NP_001276090.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICB	ENST00000538442.5	TSL:2	c.-27+3047C>A		intron	N/A	ENSP00000442345.1
	MICB	ENST00000252229.7	TSL:1 MANE Select	c.-152C>A		upstream_gene	N/A	ENSP00000252229.6
	MICB	ENST00000399150.7	TSL:1	c.-152C>A		upstream_gene	N/A	ENSP00000382103.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 309368 Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0 AN XY: 165216

African (AFR) AF: 0.00 AC: 0 AN: 5012

American (AMR) AF: 0.00 AC: 0 AN: 7756

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6838

East Asian (EAS) AF: 0.00 AC: 0 AN: 9420

South Asian (SAS) AF: 0.00 AC: 0 AN: 40086

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 23382

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2416

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 199700

Other (OTH) AF: 0.00 AC: 0 AN: 14758

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 21852

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.7
DANN	Benign	0.34
PhyloP100		0.27
PromoterAI		-0.081	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3828914; hg19: chr6-31465819;