rs2239802

Variant names:

• chr6-32444069-C-A
• rs2239802
• NM_019111.5:c.*11+148C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-32444069-C-A
• chr6-32444069-C-G
• chr6-32444069-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_019111.5(HLA-DRA):​c.*11+148C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HLA-DRA NM_019111.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350
• Publications: 44 publications found

Genes affected

HLA-DRA (HGNC:4947): (major histocompatibility complex, class II, DR alpha) HLA-DRA is one of the HLA class II alpha chain paralogues. This class II molecule is a heterodimer consisting of an alpha and a beta chain, both anchored in the membrane. This molecule is expressed on the surface of various antigen presenting cells such as B lymphocytes, dendritic cells, and monocytes/macrophages, and plays a central role in the immune system and response by presenting peptides derived from extracellular proteins, in particular, pathogen-derived peptides to T cells. The alpha chain is approximately 33-35 kDa and its gene contains 5 exons. Exon 1 encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, and exon 4 encodes the transmembrane domain and the cytoplasmic tail. DRA does not have polymorphisms in the peptide binding part and acts as the sole alpha chain for DRB1, DRB3, DRB4 and DRB5. [provided by RefSeq, Aug 2020]

ENSG00000299747 (HGNC:):

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DRA	NM_019111.5	c.*11+148C>A		intron_variant	Intron 4 of 4	ENST00000395388.7	NP_061984.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DRA	ENST00000395388.7	c.*11+148C>A		intron_variant	Intron 4 of 4	6	NM_019111.5	ENSP00000378786.2
HLA-DRA	ENST00000374982.5	c.*11+148C>A		intron_variant	Intron 4 of 4	6		ENSP00000364121.5
ENSG00000299747	ENST00000766007.1	n.163-5809G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 359738 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 182052

African (AFR) AF: 0.00 AC: 0 AN: 9142

American (AMR) AF: 0.00 AC: 0 AN: 9126

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10418

East Asian (EAS) AF: 0.00 AC: 0 AN: 23954

South Asian (SAS) AF: 0.00 AC: 0 AN: 10548

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24488

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1604

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 249572

Other (OTH) AF: 0.00 AC: 0 AN: 20886

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 22584

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.8
DANN	Benign	0.57
PhyloP100		0.35

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

Other links and lift over

dbSNP: rs2239802; hg19: chr6-32411846;