rs9268832

Variant names:

• chr6-32460012-T-C
• rs9268832
• ENST00000449413.1:n.152A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000449413.1(HLA-DRB9):​n.152A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 518,956 control chromosomes in the GnomAD database, including 98,045 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 0.60 (27469 hom., cov: 31)
  • Exomes 𝑓: 0.61 (70576 hom.)
• Consequence: HLA-DRB9 ENST00000449413.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.43
• Publications: 82 publications found

Genes affected

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

ENSG00000299747 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DRB9		n.32460012T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DRB9	ENST00000449413.1	n.152A>G		non_coding_transcript_exon_variant	Exon 2 of 2	6
ENSG00000299747	ENST00000766009.1	n.335A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000299747	ENST00000766007.1	n.-31A>G		upstream_gene_variant
ENSG00000299747	ENST00000766008.1	n.-28A>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90683 AN: 151852 Hom.: 27452 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.637

GnomAD2 exomes AF: 0.614 AC: 141216 AN: 229982 AF XY: 0.620

Gnomad AFR exome AF: 0.581

Gnomad AMR exome AF: 0.622

Gnomad ASJ exome AF: 0.755

Gnomad EAS exome AF: 0.586

Gnomad FIN exome AF: 0.508

Gnomad NFE exome AF: 0.601

Gnomad OTH exome AF: 0.631

GnomAD4 exome AF: 0.615 AC: 225664 AN: 366986 Hom.: 70576 Cov.: 0 AF XY: 0.623 AC XY: 131049 AN XY: 210406

African (AFR) AF: 0.573 AC: 6027 AN: 10510

American (AMR) AF: 0.625 AC: 22681 AN: 36302

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 8828 AN: 11744

East Asian (EAS) AF: 0.587 AC: 7732 AN: 13172

South Asian (SAS) AF: 0.678 AC: 45263 AN: 66802

European-Finnish (FIN) AF: 0.503 AC: 8618 AN: 17150

Middle Eastern (MID) AF: 0.736 AC: 2098 AN: 2852

European-Non Finnish (NFE) AF: 0.597 AC: 114462 AN: 191842

Other (OTH) AF: 0.599 AC: 9955 AN: 16612

GnomAD4 genome AF: 0.597 AC: 90750 AN: 151970 Hom.: 27469 Cov.: 31 AF XY: 0.596 AC XY: 44298 AN XY: 74276

African (AFR) AF: 0.574 AC: 23780 AN: 41458

American (AMR) AF: 0.664 AC: 10149 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2627 AN: 3468

East Asian (EAS) AF: 0.566 AC: 2908 AN: 5142

South Asian (SAS) AF: 0.649 AC: 3126 AN: 4818

European-Finnish (FIN) AF: 0.504 AC: 5317 AN: 10540

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40588 AN: 67948

Other (OTH) AF: 0.632 AC: 1337 AN: 2114

Alfa AF: 0.599 Hom.: 94599

Bravo AF: 0.611

Asia WGS AF: 0.548 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.25
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs9268832; hg19: chr6-32427789;