rs9268856

chr6-32461942-C-Achr6-32461942-C-T

Variant summary

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

The ENST00000449413.1(HLA-DRB9):n.77-1855G>T 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 0.288 in 150,620 control chromosomes in the GnomAD database, including 6,317 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 (6317 hom., cov: 32)
• Consequence: HLA-DRB9 ENST00000449413.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 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.77-1855G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43304 AN: 150526 Hom.: 6313 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.288 AC: 43336 AN: 150620 Hom.: 6317 Cov.: 32 AF XY: 0.289 AC XY: 21203 AN XY: 73406

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.288

Alfa AF: 0.232 Hom.: 1921

Bravo AF: 0.281

Asia WGS AF: 0.278 AC: 965 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.3
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9268856; hg19: chr6-32429719;