chr6-32460409-G-C

Position:

• chr6-32460409-G-C

Variant summary

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

The ENST00000449413.1(HLA-DRB9):​n.77-322C>G 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 0.668 in 151,984 control chromosomes in the GnomAD database, including 34,271 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 0.67 (34271 hom., cov: 31)
• Consequence: HLA-DRB9 ENST00000449413.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.821

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.695 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.77-322C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101434 AN: 151866 Hom.: 34241 Cov.: 31

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.668 AC: 101507 AN: 151984 Hom.: 34271 Cov.: 31 AF XY: 0.668 AC XY: 49657 AN XY: 74286

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.671

Alfa AF: 0.674 Hom.: 17408

Bravo AF: 0.666

Asia WGS AF: 0.604 AC: 2105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.68
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6923504; hg19: chr6-32428186;