rs9268858

Positions:

• chr6-32461981-T-C

Variant summary

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

The ENST00000449413.1(HLA-DRB9):​n.77-1894A>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 0.292 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39

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=-0.93).
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLA-DRB9	ENST00000449413.1	n.77-1894A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.306

Alfa AF: 0.310 Hom.: 2250

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9268858; hg19: chr6-32429758;