6-32461866-T-C

Variant names:

• chr6-32461866-T-C
• rs9268853
• ENST00000449413.1:n.77-1779A>G

Variant summary

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

The ENST00000449413.1(HLA-DRB9):​n.77-1779A>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 152,094 control chromosomes in the GnomAD database, including 6,797 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 (6797 hom., cov: 33)
• Consequence: HLA-DRB9 ENST00000449413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 112 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449413.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DRB9	ENST00000449413.1	TSL:6	n.77-1779A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44207 AN: 151976 Hom.: 6796 Cov.: 33

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.343

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: 44234 AN: 152094 Hom.: 6797 Cov.: 33 AF XY: 0.287 AC XY: 21324 AN XY: 74342

African (AFR) AF: 0.226 AC: 9383 AN: 41474

American (AMR) AF: 0.358 AC: 5475 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1524 AN: 3472

East Asian (EAS) AF: 0.345 AC: 1781 AN: 5168

South Asian (SAS) AF: 0.258 AC: 1246 AN: 4826

European-Finnish (FIN) AF: 0.235 AC: 2480 AN: 10562

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21243 AN: 67998

Other (OTH) AF: 0.304 AC: 642 AN: 2112

Alfa AF: 0.309 Hom.: 23304

Bravo AF: 0.307

Asia WGS AF: 0.251 AC: 874 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.85
DANN	Benign	0.55
PhyloP100		-2.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9268853;

hg19: chr6-32429643;