Genetic Variant HLA-C:p.Arg121Gly (chr6-31271331-T-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_002117.6(HLA-C):c.361A>G(p.Arg121Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 5)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

HLA-C
NM_002117.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -10.4

Publications

28 publications found

Variant links:

Genes affected

HLA-C (HGNC:4933): (major histocompatibility complex, class I, C) HLA-C belongs to the HLA class I heavy chain paralogues. This class I molecule is a heterodimer consisting of a heavy chain and a light chain (beta-2 microglobulin). The heavy chain is anchored in the membrane. Class I molecules play a central role in the immune system by presenting peptides derived from endoplasmic reticulum lumen. They are expressed in nearly all cells. The heavy chain is approximately 45 kDa and its gene contains 8 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the alpha1 and alpha2 domain, which both bind the peptide, exon 4 encodes the alpha3 domain, exon 5 encodes the transmembrane region, and exons 6 and 7 encode the cytoplasmic tail. Polymorphisms within exon 2 and exon 3 are responsible for the peptide binding specificity of each class one molecule. Typing for these polymorphisms is routinely done for bone marrow and kidney transplantation. About 6000 HLA-C alleles have been described. The HLA system plays an important role in the occurrence and outcome of infectious diseases, including those caused by the malaria parasite, the human immunodeficiency virus (HIV), and the severe acute respiratory syndrome coronavirus (SARS-CoV). The structural spike and the nucleocapsid proteins of the novel coronavirus SARS-CoV-2, which causes coronavirus disease 2019 (COVID-19), are reported to contain multiple Class I epitopes with predicted HLA restrictions. Individual HLA genetic variation may help explain different immune responses to a virus across a population.[provided by RefSeq, Aug 2020]

HLA-C links:

ENSG00000298396 (HGNC:):

ENSG00000298396 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (MetaRNN=0.11424339).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-C	NM_002117.6 link	c.361A>G	p.Arg121Gly	missense_variant	Exon 3 of 8	ENST00000376228.10	NP_002108.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-C	ENST00000376228.10 link	c.361A>G	p.Arg121Gly	missense_variant	Exon 3 of 8	6	NM_002117.6	ENSP00000365402.5

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

59400

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00000428

AC:

AN:

233900

AF XY:

0.00000780

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

894932

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

451244

African (AFR)

AF:

0.00

AC:

AN:

17730

American (AMR)

AF:

0.00

AC:

AN:

28114

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

12966

East Asian (EAS)

AF:

0.00

AC:

AN:

20554

South Asian (SAS)

AF:

0.00

AC:

AN:

61540

European-Finnish (FIN)

AF:

0.00

AC:

AN:

28498

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2488

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

686696

Other (OTH)

AF:

0.00

AC:

AN:

36346

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

59400

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

28256

African (AFR)

AF:

0.00

AC:

AN:

12240

American (AMR)

AF:

0.00

AC:

AN:

5414

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

746

East Asian (EAS)

AF:

0.00

AC:

AN:

1532

South Asian (SAS)

AF:

0.00

AC:

AN:

1628

European-Finnish (FIN)

AF:

0.00

AC:

AN:

4332

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

32294

Other (OTH)

AF:

0.00

AC:

AN:

690

Alfa

AF:

0.000142

Hom.:

460

ExAC

AF:

0.0000333

AC:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.18

BayesDel_addAF

Benign

-0.19

BayesDel_noAF

Benign

-0.42

CADD

Benign

4.4

(source)

DANN

Benign

0.75

DEOGEN2

Benign

0.039

T;.

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.8

FATHMM_MKL

Benign

0.011

LIST_S2

Benign

0.0066

T;T

M_CAP

Benign

0.0013

MetaRNN

Benign

0.11

T;T

MetaSVM

Benign

-1.0

PhyloP100

-10

PrimateAI

Benign

0.21

PROVEAN

Benign

-1.5

N;N

REVEL

Benign

0.20

Sift

Benign

0.057

T;D

Sift4G

Benign

0.44

T;T

Polyphen

0.58

P;P

Vest4

0.21

MutPred

0.23

Loss of phosphorylation at S123 (P = 0.0905);Loss of phosphorylation at S123 (P = 0.0905);

MVP

0.11

MPC

1.4

ClinPred

0.13

GERP RS

-5.6

gMVP

0.59

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.11

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over