6-31511349-C-T

Variant names:

• chr6-31511349-C-T
• rs2246626
• NM_005931.5:c.*1440C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005931.5(MICB):​c.*1440C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 151,984 control chromosomes in the GnomAD database, including 16,078 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 0.45 (16078 hom., cov: 32)
• Consequence: MICB NM_005931.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICB	NM_005931.5	c.*1440C>T		downstream_gene_variant		ENST00000252229.7	NP_005922.2
MICB	NM_001289160.2	c.*1440C>T		downstream_gene_variant			NP_001276089.1
MICB	NM_001289161.2	c.*1440C>T		downstream_gene_variant			NP_001276090.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICB	ENST00000252229.7	c.*1440C>T		downstream_gene_variant		1	NM_005931.5	ENSP00000252229.6
MICB	ENST00000399150.7	c.*1440C>T		downstream_gene_variant		1		ENSP00000382103.3
MICB	ENST00000538442.5	c.*1440C>T		downstream_gene_variant		2		ENSP00000442345.1

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69072 AN: 151866 Hom.: 16060 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.482

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.455 AC: 69126 AN: 151984 Hom.: 16078 Cov.: 32 AF XY: 0.458 AC XY: 34008 AN XY: 74300

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.487

Alfa AF: 0.432 Hom.: 2595

Bravo AF: 0.471

Asia WGS AF: 0.495 AC: 1719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2246626; hg19: chr6-31479126;