ENST00000449413.1:n.76+1694C>T

Variant names:

• chr6-32471731-G-A
• rs2187823
• ENST00000449413.1:n.76+1694C>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.76+1694C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 143,120 control chromosomes in the GnomAD database, including 4,566 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 0.28 (4566 hom., cov: 34)
• Consequence: HLA-DRB9 ENST00000449413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139
• Publications: 27 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 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+1694C>T		intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.284 AC: 40664 AN: 143006 Hom.: 4564 Cov.: 34

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.246

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.284 AC: 40695 AN: 143120 Hom.: 4566 Cov.: 34 AF XY: 0.284 AC XY: 19873 AN XY: 69984

African (AFR) AF: 0.342 AC: 13139 AN: 38414

American (AMR) AF: 0.271 AC: 3852 AN: 14228

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 785 AN: 3212

East Asian (EAS) AF: 0.243 AC: 1196 AN: 4914

South Asian (SAS) AF: 0.246 AC: 1091 AN: 4428

European-Finnish (FIN) AF: 0.333 AC: 3388 AN: 10170

Middle Eastern (MID) AF: 0.250 AC: 61 AN: 244

European-Non Finnish (NFE) AF: 0.255 AC: 16522 AN: 64692

Other (OTH) AF: 0.283 AC: 549 AN: 1940

Alfa AF: 0.268 Hom.: 17058

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.6
DANN	Benign	0.55
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2187823; hg19: chr6-32439508;