rs2242955

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005931.5(MICB):​c.613+73G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 1,510,080 control chromosomes in the GnomAD database, including 10,845 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 0.12 ( 1153 hom., cov: 32)
Exomes 𝑓: 0.12 ( 9692 hom. )

Consequence

MICB
NM_005931.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.26
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MICBNM_005931.5 linkuse as main transcriptc.613+73G>A intron_variant ENST00000252229.7
MICBNM_001289160.2 linkuse as main transcriptc.517+73G>A intron_variant
MICBNM_001289161.2 linkuse as main transcriptc.484+73G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MICBENST00000252229.7 linkuse as main transcriptc.613+73G>A intron_variant 1 NM_005931.5 P1Q29980-1
MICBENST00000399150.7 linkuse as main transcriptc.484+73G>A intron_variant 1 Q29980-2
MICBENST00000538442.5 linkuse as main transcriptc.517+73G>A intron_variant 2
MICBENST00000494577.1 linkuse as main transcriptn.496+73G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.120
AC:
18237
AN:
152098
Hom.:
1152
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.132
Gnomad AMI
AF:
0.0208
Gnomad AMR
AF:
0.0858
Gnomad ASJ
AF:
0.0493
Gnomad EAS
AF:
0.131
Gnomad SAS
AF:
0.153
Gnomad FIN
AF:
0.149
Gnomad MID
AF:
0.130
Gnomad NFE
AF:
0.117
Gnomad OTH
AF:
0.119
GnomAD4 exome
AF:
0.118
AC:
160086
AN:
1357864
Hom.:
9692
AF XY:
0.119
AC XY:
79723
AN XY:
671802
show subpopulations
Gnomad4 AFR exome
AF:
0.131
Gnomad4 AMR exome
AF:
0.0778
Gnomad4 ASJ exome
AF:
0.0537
Gnomad4 EAS exome
AF:
0.134
Gnomad4 SAS exome
AF:
0.145
Gnomad4 FIN exome
AF:
0.151
Gnomad4 NFE exome
AF:
0.117
Gnomad4 OTH exome
AF:
0.113
GnomAD4 genome
AF:
0.120
AC:
18254
AN:
152216
Hom.:
1153
Cov.:
32
AF XY:
0.120
AC XY:
8966
AN XY:
74426
show subpopulations
Gnomad4 AFR
AF:
0.132
Gnomad4 AMR
AF:
0.0863
Gnomad4 ASJ
AF:
0.0493
Gnomad4 EAS
AF:
0.132
Gnomad4 SAS
AF:
0.153
Gnomad4 FIN
AF:
0.149
Gnomad4 NFE
AF:
0.117
Gnomad4 OTH
AF:
0.118
Alfa
AF:
0.107
Hom.:
776
Bravo
AF:
0.116
Asia WGS
AF:
0.145
AC:
507
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.46
DANN
Benign
0.67

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

Publications

LitVar

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

Other links and lift over

dbSNP: rs2242955; hg19: chr6-31474280; COSMIC: COSV52856221; API