6-32460508-C-T

Variant names:

• chr6-32460508-C-T
• rs6903608
• ENST00000449413.1:n.77-421G>A

Variant summary

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

The ENST00000449413.1(HLA-DRB9):​n.77-421G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 152,056 control chromosomes in the GnomAD database, including 34,257 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 (34257 hom., cov: 32)
• Consequence: HLA-DRB9 ENST00000449413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

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=-0.96).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DRB9	ENST00000449413.1	n.77-421G>A		intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101450 AN: 151938 Hom.: 34227 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.619

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: 101523 AN: 152056 Hom.: 34257 Cov.: 32 AF XY: 0.668 AC XY: 49671 AN XY: 74336

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.672

Alfa AF: 0.673 Hom.: 63331

Bravo AF: 0.666

Asia WGS AF: 0.598 AC: 2084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.9
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6903608; hg19: chr6-32428285;