Genetic Variant HLA-DPB2:n.364+4626C>A (chr6-33121846-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000470997.1(HLA-DPB2):n.364+4626C>A variant causes a intron 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
ENST00000470997.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.915

Publications

32 publications found

Variant links:

Genes affected

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

HLA-DPB2 links:

ENSG00000291111 (HGNC:):

ENSG00000291111 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HLA-DPB2	NR_001435.2 link	n.364+4626C>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HLA-DPB2	ENST00000470997.1 link	n.364+4626C>A	intron_variant	Intron 2 of 4	6
ENSG00000291111	ENST00000782892.1 link	n.429+4626C>A	intron_variant	Intron 2 of 2
ENSG00000291111	ENST00000782893.1 link	n.403+4626C>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.300

AC:

45552

AN:

151970

Hom.:

7063

Cov.:

show subpopulations

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.:

AF XY:

0.300

AC XY:

22337

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.241

AC:

10007

AN:

41476

American (AMR)

AF:

0.249

AC:

3809

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.407

AC:

1411

AN:

3466

East Asian (EAS)

AF:

0.199

AC:

1030

AN:

5176

South Asian (SAS)

AF:

0.527

AC:

2536

AN:

4816

European-Finnish (FIN)

AF:

0.281

AC:

2978

AN:

10580

Middle Eastern (MID)

AF:

0.415

AC:

122

AN:

294

European-Non Finnish (NFE)

AF:

0.334

AC:

22706

AN:

67974

Other (OTH)

AF:

0.306

AC:

644

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1636

3273

4909

6546

8182

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.317

Hom.:

7203

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

(source)

DANN

Benign

0.53

PhyloP100

-0.92

Splicing

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

Publications

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6-33121846-C-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over