6-32462585-C-G

Position:

• chr6-32462585-C-G

Variant summary

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

The ENST00000449413.1(HLA-DRB9):​n.77-2498G>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 0.286 in 152,064 control chromosomes in the GnomAD database, including 6,397 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 (6397 hom., cov: 31)
• Consequence: HLA-DRB9 ENST00000449413.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419

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=-0.88).
• 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.77-2498G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43531 AN: 151946 Hom.: 6393 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.286 AC: 43564 AN: 152064 Hom.: 6397 Cov.: 31 AF XY: 0.287 AC XY: 21334 AN XY: 74330

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.285

Alfa AF: 0.262 Hom.: 2977

Bravo AF: 0.282

Asia WGS AF: 0.278 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4428528; hg19: chr6-32430362;