rs9268858

Variant names:

• chr6-32461981-T-C
• rs9268858
• ENST00000449413.1:n.77-1894A>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.77-1894A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 151,090 control chromosomes in the GnomAD database, including 6,785 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 0.29 (6785 hom., cov: 30)
• Consequence: HLA-DRB9 ENST00000449413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39
• Publications: 44 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.351 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.77-1894A>G		intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44051 AN: 151000 Hom.: 6784 Cov.: 30

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.292 AC: 44079 AN: 151090 Hom.: 6785 Cov.: 30 AF XY: 0.288 AC XY: 21236 AN XY: 73710

African (AFR) AF: 0.226 AC: 9331 AN: 41214

American (AMR) AF: 0.359 AC: 5460 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1522 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1785 AN: 5174

South Asian (SAS) AF: 0.260 AC: 1246 AN: 4794

European-Finnish (FIN) AF: 0.241 AC: 2420 AN: 10050

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.312 AC: 21211 AN: 67886

Other (OTH) AF: 0.306 AC: 644 AN: 2104

Alfa AF: 0.296 Hom.: 3937

Bravo AF: 0.307

Asia WGS AF: 0.251 AC: 872 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.56
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs9268858; hg19: chr6-32429758;