rs9268852

Variant names:

• chr6-32461817-A-G
• rs9268852
• ENST00000449413.1:n.77-1730T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-32461817-A-G
• chr6-32461817-A-T

Variant summary

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

The ENST00000449413.1(HLA-DRB9):​n.77-1730T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 152,070 control chromosomes in the GnomAD database, including 25,451 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 0.58 (25451 hom., cov: 33)
• Consequence: HLA-DRB9 ENST00000449413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.621 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.77-1730T>C		intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87679 AN: 151952 Hom.: 25432 Cov.: 33

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.577 AC: 87738 AN: 152070 Hom.: 25451 Cov.: 33 AF XY: 0.574 AC XY: 42643 AN XY: 74336

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.591

Alfa AF: 0.559 Hom.: 9202

Bravo AF: 0.588

Asia WGS AF: 0.529 AC: 1839 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	2.9
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9268852; hg19: chr6-32429594;