6-29941979-G-T

Position:

• chr6-29941979-G-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000706894(HLA-A):​c.-268G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 148,904 control chromosomes in the GnomAD database, including 1,283 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 0.13 (1283 hom., cov: 33)
  • Exomes 𝑓: 0.11 (114 hom.)
  • Failed GnomAD Quality Control
• Consequence: HLA-A ENST00000706894 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379

Genes affected

HLA-A (HGNC:4931): (major histocompatibility complex, class I, A) HLA-A 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 the endoplasmic reticulum lumen so that they can be recognized by cytotoxic T cells. They are expressed in nearly all cells. The heavy chain is approximately 45 kDa and its gene contains 8 exons. Exon 1 encodes the leader peptide, exons 2 and 3 encode the alpha1 and alpha2 domains, 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. More than 6000 HLA-A 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-A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901298	XR_007059541.1	n.813+2802C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLA-A	ENST00000706894	c.-268G>T		5_prime_UTR_premature_start_codon_gain_variant	1/8			ENSP00000516610.1
HLA-A	ENST00000706898	c.-268G>T		5_prime_UTR_premature_start_codon_gain_variant	1/9			ENSP00000516611.1
HLA-A	ENST00000706904	c.-268G>T		5_prime_UTR_premature_start_codon_gain_variant	1/9			ENSP00000516615.1

Frequencies

GnomAD3 genomes AF: 0.128 AC: 18980 AN: 148786 Hom.: 1278 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0973

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.137

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.112 AC: 1331 AN: 11882 Hom.: 114 Cov.: 0 AF XY: 0.114 AC XY: 761 AN XY: 6700

Gnomad4 AFR exome AF: 0.107

Gnomad4 AMR exome AF: 0.0966

Gnomad4 ASJ exome AF: 0.0769

Gnomad4 EAS exome AF: 0.270

Gnomad4 SAS exome AF: 0.119

Gnomad4 FIN exome AF: 0.0893

Gnomad4 NFE exome AF: 0.0966

Gnomad4 OTH exome AF: 0.103

GnomAD4 genome AF: 0.128 AC: 18992 AN: 148904 Hom.: 1283 Cov.: 33 AF XY: 0.129 AC XY: 9403 AN XY: 72710

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.0973

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.144

Alfa AF: 0.0785 Hom.: 620

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.53
DANN	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.26		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.26		Position offset: -13

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

Publications

LitVar

Other links and lift over

dbSNP: rs9260109; hg19: chr6-29909756;