6-32464300-G-C

Variant names:

• chr6-32464300-G-C
• rs9268905
• ENST00000449413.1:n.77-4213C>G

Variant summary

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

The ENST00000449413.1(HLA-DRB9):​n.77-4213C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,040 control chromosomes in the GnomAD database, including 6,794 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 (6794 hom., cov: 32)
• Consequence: HLA-DRB9 ENST00000449413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.976

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=-0.94).
• 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.77-4213C>G		intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44176 AN: 151922 Hom.: 6793 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.291 AC: 44203 AN: 152040 Hom.: 6794 Cov.: 32 AF XY: 0.287 AC XY: 21313 AN XY: 74328

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.304

Alfa AF: 0.153 Hom.: 255

Bravo AF: 0.307

Asia WGS AF: 0.251 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9268905; hg19: chr6-32432077;