Genetic Variant HLA-DRB9:n.193G>A (chr6-32459971-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000449413.1(HLA-DRB9):n.193G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.523 in 519,710 control chromosomes in the GnomAD database, including 72,800 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 0.51 ( 20255 hom., cov: 32)

Exomes 𝑓: 0.53 ( 52545 hom. )

Consequence

HLA-DRB9
ENST00000449413.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.97

Variant links:

Genes affected

HLA-DRB9 (HGNC:4957): (major histocompatibility complex, class II, DR beta 9 (pseudogene))

HLA-DRB9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DRB9		n.32459971C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DRB9	ENST00000449413.1 link	n.193G>A		non_coding_transcript_exon_variant	Exon 2 of 2	6

Frequencies

GnomAD3 genomes

AF:

0.512

AC:

77774

AN:

151910

Hom.:

20232

Cov.:

show subpopulations

Gnomad AFR

AF:

0.514

Gnomad AMI

AF:

0.382

Gnomad AMR

AF:

0.609

Gnomad ASJ

AF:

0.630

Gnomad EAS

AF:

0.555

Gnomad SAS

AF:

0.505

Gnomad FIN

AF:

0.432

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.492

Gnomad OTH

AF:

0.535

GnomAD3 exomes

AF:

0.541

AC:

124860

AN:

230910

Hom.:

34814

AF XY:

0.538

AC XY:

68535

AN XY:

127480

show subpopulations

Gnomad AFR exome

AF:

0.519

Gnomad AMR exome

AF:

0.672

Gnomad ASJ exome

AF:

0.634

Gnomad EAS exome

AF:

0.579

Gnomad SAS exome

AF:

0.544

Gnomad FIN exome

AF:

0.429

Gnomad NFE exome

AF:

0.498

Gnomad OTH exome

AF:

0.539

GnomAD4 exome

AF:

0.527

AC:

193725

AN:

367682

Hom.:

52545

Cov.:

AF XY:

0.527

AC XY:

111143

AN XY:

210772

show subpopulations

Gnomad4 AFR exome

AF:

0.512

Gnomad4 AMR exome

AF:

0.672

Gnomad4 ASJ exome

AF:

0.635

Gnomad4 EAS exome

AF:

0.562

Gnomad4 SAS exome

AF:

0.549

Gnomad4 FIN exome

AF:

0.427

Gnomad4 NFE exome

AF:

0.493

Gnomad4 OTH exome

AF:

0.508

GnomAD4 genome

AF:

0.512

AC:

77846

AN:

152028

Hom.:

20255

Cov.:

AF XY:

0.512

AC XY:

38069

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.514

Gnomad4 AMR

AF:

0.610

Gnomad4 ASJ

AF:

0.630

Gnomad4 EAS

AF:

0.556

Gnomad4 SAS

AF:

0.506

Gnomad4 FIN

AF:

0.432

Gnomad4 NFE

AF:

0.492

Gnomad4 OTH

AF:

0.534

Alfa

AF:

0.511

Hom.:

28694

Bravo

AF:

0.528

Asia WGS

AF:

0.495

AC:

1722

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

DANN

Benign

0.72

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over