ENST00000449413.1:n.76+1809T>G

Variant names:

• chr6-32471616-A-C
• rs9405040
• ENST00000449413.1:n.76+1809T>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.76+1809T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 151,042 control chromosomes in the GnomAD database, including 1,876 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 0.26 (1876 hom., cov: 35)
• Consequence: HLA-DRB9 ENST00000449413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.674
• Publications: 18 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.302 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.76+1809T>G		intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38721 AN: 150922 Hom.: 1873 Cov.: 35

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.257 AC: 38751 AN: 151042 Hom.: 1876 Cov.: 35 AF XY: 0.254 AC XY: 18728 AN XY: 73846

African (AFR) AF: 0.208 AC: 8585 AN: 41312

American (AMR) AF: 0.310 AC: 4679 AN: 15110

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1307 AN: 3434

East Asian (EAS) AF: 0.299 AC: 1535 AN: 5134

South Asian (SAS) AF: 0.232 AC: 1108 AN: 4780

European-Finnish (FIN) AF: 0.213 AC: 2237 AN: 10504

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.272 AC: 18363 AN: 67498

Other (OTH) AF: 0.270 AC: 562 AN: 2082

Alfa AF: 0.242 Hom.: 1371

Asia WGS AF: 0.241 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.49
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs9405040; hg19: chr6-32439393;