chr6-32461942-C-A

Variant names:

• chr6-32461942-C-A
• rs9268856
• ENST00000449413.1:n.77-1855G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000449413.1(HLA-DRB9):​n.77-1855G>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803
• Publications: 37 publications found

Genes affected

HLA-DRB9 (HGNC:4957): (major histocompatibility complex, class II, DR beta 9 (pseudogene))

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DRB9	ENST00000449413.1	n.77-1855G>T		intron_variant	Intron 1 of 1	6

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

African (AFR) AF: 0.342 AC: 14057 AN: 41052

American (AMR) AF: 0.275 AC: 4161 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3464

East Asian (EAS) AF: 0.246 AC: 1262 AN: 5134

South Asian (SAS) AF: 0.239 AC: 1148 AN: 4804

European-Finnish (FIN) AF: 0.370 AC: 3710 AN: 10014

Middle Eastern (MID) AF: 0.222 AC: 64 AN: 288

European-Non Finnish (NFE) AF: 0.257 AC: 17401 AN: 67714

Other (OTH) AF: 0.288 AC: 601 AN: 2090

Alfa AF: 0.262 Hom.: 11491

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
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs9268856; hg19: chr6-32429719;