rs9268852

Positions:

• 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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-DRB9	ENST00000449413.1	n.77-1730T>C		intron_variant, non_coding_transcript_variant

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;