rs9268880

Variant names:

• chr6-32463581-T-G
• rs9268880
• ENST00000449413.1:n.77-3494A>C

Variant summary

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

The ENST00000449413.1(HLA-DRB9):​n.77-3494A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,112 control chromosomes in the GnomAD database, including 34,423 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 0.67 (34423 hom., cov: 32)
• Consequence: HLA-DRB9 ENST00000449413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 22 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DRB9	ENST00000449413.1	n.77-3494A>C		intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101730 AN: 151994 Hom.: 34394 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.669 AC: 101801 AN: 152112 Hom.: 34423 Cov.: 32 AF XY: 0.670 AC XY: 49820 AN XY: 74380

African (AFR) AF: 0.619 AC: 25670 AN: 41468

American (AMR) AF: 0.706 AC: 10796 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2477 AN: 3472

East Asian (EAS) AF: 0.624 AC: 3226 AN: 5168

South Asian (SAS) AF: 0.579 AC: 2791 AN: 4820

European-Finnish (FIN) AF: 0.798 AC: 8452 AN: 10592

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46113 AN: 67984

Other (OTH) AF: 0.675 AC: 1426 AN: 2114

Alfa AF: 0.674 Hom.: 88656

Bravo AF: 0.667

Asia WGS AF: 0.604 AC: 2106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.0
DANN	Benign	0.72
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs9268880; hg19: chr6-32431358;