6-33128989-A-T

Variant names:

• chr6-33128989-A-T
• rs3117004
• ENST00000782902.1:n.1381A>T

Variant summary

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

The ENST00000782902.1(ENSG00000291111):​n.1381A>T variant causes a non coding transcript exon 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000291111 ENST00000782902.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 0 publications found

Genes affected

ENSG00000291111 (HGNC:):

HLA-DPB2 (HGNC:4941): (major histocompatibility complex, class II, DP beta 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=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DPB2	NR_001435.2	n.757-76A>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291111	ENST00000782902.1	n.1381A>T		non_coding_transcript_exon_variant	Exon 2 of 2
HLA-DPB2	ENST00000470997.1	n.757-76A>T		intron_variant	Intron 4 of 4	6
ENSG00000291111	ENST00000782892.1	n.429+11769A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 234418 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 136300

African (AFR) AF: 0.00 AC: 0 AN: 5682

American (AMR) AF: 0.00 AC: 0 AN: 23348

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6516

East Asian (EAS) AF: 0.00 AC: 0 AN: 7044

South Asian (SAS) AF: 0.00 AC: 0 AN: 41164

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 18508

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2400

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 119018

Other (OTH) AF: 0.00 AC: 0 AN: 10738

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.2
DANN	Benign	0.48
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3117004; hg19: chr6-33096766;