rs9269081

Positions:

• chr6-32473323-A-C
• chr6-32473323-A-G

Variant summary

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

The ENST00000449413.1(HLA-DRB9):​n.76+102T>G 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 0.701 in 739,836 control chromosomes in the GnomAD database, including 184,426 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 0.69 (36052 hom., cov: 31)
  • Exomes 𝑓: 0.70 (148374 hom.)
• Consequence: HLA-DRB9 ENST00000449413.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.96

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLA-DRB9	ENST00000449413.1	n.76+102T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.685 AC: 104046 AN: 151818 Hom.: 36018 Cov.: 31

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.698

GnomAD4 exome AF: 0.705 AC: 414365 AN: 587900 Hom.: 148374 AF XY: 0.692 AC XY: 221018 AN XY: 319378

Gnomad4 AFR exome AF: 0.654

Gnomad4 AMR exome AF: 0.817

Gnomad4 ASJ exome AF: 0.733

Gnomad4 EAS exome AF: 0.713

Gnomad4 SAS exome AF: 0.546

Gnomad4 FIN exome AF: 0.794

Gnomad4 NFE exome AF: 0.711

Gnomad4 OTH exome AF: 0.702

GnomAD4 genome AF: 0.685 AC: 104125 AN: 151936 Hom.: 36052 Cov.: 31 AF XY: 0.686 AC XY: 50923 AN XY: 74254

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.736

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.696

Alfa AF: 0.709 Hom.: 16905

Bravo AF: 0.685

Asia WGS AF: 0.633 AC: 2207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.13
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9269081; hg19: chr6-32441100;