chr6-33121846-C-A

Position:

• chr6-33121846-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_001435.2(HLA-DPB2):​n.364+4626C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,088 control chromosomes in the GnomAD database, including 7,063 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 0.30 (7063 hom., cov: 32)
• Consequence: HLA-DPB2 NR_001435.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.915

Genes affected

HLA-DPB2 (HGNC:4941): (major histocompatibility complex, class II, DP beta 2 (pseudogene))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HLA-DPB2	NR_001435.2	n.364+4626C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-DPB2	ENST00000470997.1	n.364+4626C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45552 AN: 151970 Hom.: 7063 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.308

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.300 AC: 45568 AN: 152088 Hom.: 7063 Cov.: 32 AF XY: 0.300 AC XY: 22337 AN XY: 74364

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.306

Alfa AF: 0.302 Hom.: 3847

Bravo AF: 0.288

Asia WGS AF: 0.346 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3117027; hg19: chr6-33089623;