Variant chr6-31410733-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001177519.3(MICA):c.261G>A(p.Arg87=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0629 in 1,604,506 control chromosomes in the GnomAD database, including 3,853 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 0.066 ( 437 hom., cov: 32)

Exomes 𝑓: 0.063 ( 3416 hom. )

Consequence

MICA
NM_001177519.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.149

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 Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP7

Synonymous conserved (PhyloP=-0.149 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
MICA	NM_001177519.3 linkuse as main transcript	c.261G>A	p.Arg87=	synonymous_variant	2/6	ENST00000449934.7
MICA	NM_001289154.2 linkuse as main transcript	c.19G>A	p.Gly7Arg	missense_variant	2/6
MICA	NM_001289152.2 linkuse as main transcript	c.-31G>A		5_prime_UTR_variant	2/6
MICA	NM_001289153.2 linkuse as main transcript	c.-31G>A		5_prime_UTR_variant	2/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MICA	ENST00000449934.7 linkuse as main transcript	c.261G>A	p.Arg87=	synonymous_variant	2/6	1	NM_001177519.3	P1

Frequencies

GnomAD3 genomes

AF:

0.0663

AC:

10074

AN:

151852

Hom.:

433

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0697

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0607

Gnomad ASJ

AF:

0.0576

Gnomad EAS

AF:

0.0849

Gnomad SAS

AF:

0.0450

Gnomad FIN

AF:

0.0570

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.0679

Gnomad OTH

AF:

0.0747

GnomAD3 exomes

AF:

0.0641

AC:

14801

AN:

230786

Hom.:

615

AF XY:

0.0643

AC XY:

8057

AN XY:

125376

show subpopulations

Gnomad AFR exome

AF:

0.0684

Gnomad AMR exome

AF:

0.0518

Gnomad ASJ exome

AF:

0.0623

Gnomad EAS exome

AF:

0.0822

Gnomad SAS exome

AF:

0.0485

Gnomad FIN exome

AF:

0.0563

Gnomad NFE exome

AF:

0.0700

Gnomad OTH exome

AF:

0.0746

GnomAD4 exome

AF:

0.0626

AC:

90894

AN:

1452536

Hom.:

3416

Cov.:

AF XY:

0.0629

AC XY:

45433

AN XY:

721940

show subpopulations

Gnomad4 AFR exome

AF:

0.0641

Gnomad4 AMR exome

AF:

0.0520

Gnomad4 ASJ exome

AF:

0.0634

Gnomad4 EAS exome

AF:

0.107

Gnomad4 SAS exome

AF:

0.0480

Gnomad4 FIN exome

AF:

0.0564

Gnomad4 NFE exome

AF:

0.0625

Gnomad4 OTH exome

AF:

0.0644

GnomAD4 genome

AF:

0.0664

AC:

10092

AN:

151970

Hom.:

437

Cov.:

AF XY:

0.0668

AC XY:

4960

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.0696

Gnomad4 AMR

AF:

0.0607

Gnomad4 ASJ

AF:

0.0576

Gnomad4 EAS

AF:

0.0851

Gnomad4 SAS

AF:

0.0453

Gnomad4 FIN

AF:

0.0570

Gnomad4 NFE

AF:

0.0679

Gnomad4 OTH

AF:

0.0801

Alfa

AF:

0.0705

Hom.:

697

Bravo

AF:

0.0658

Asia WGS

AF:

0.104

AC:

363

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.2

DANN

Benign

0.50

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

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