rs2281389

Variant names:

• chr6-33092019-A-C
• rs2281389

Your query was ambiguous. Multiple possible variants found:

• chr6-33092019-A-C
• chr6-33092019-A-G
• chr6-33092019-A-T

Variant summary

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

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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HLA-DPA2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 0 publications found

Genes affected

HLA-DPA2 (HGNC:4939): (major histocompatibility complex, class II, DP alpha 2 (pseudogene))

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=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DPA2		n.33092019A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DPA2	ENST00000433582.1	n.582+100T>G		intron_variant	Intron 3 of 3	6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 3836 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2238

African (AFR) AF: 0.00 AC: 0 AN: 78

American (AMR) AF: 0.00 AC: 0 AN: 98

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 80

East Asian (EAS) AF: 0.00 AC: 0 AN: 234

South Asian (SAS) AF: 0.00 AC: 0 AN: 158

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 706

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 28

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2136

Other (OTH) AF: 0.00 AC: 0 AN: 318

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.78
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs2281389; hg19: chr6-33059796;