rs2187823

Variant names:

• chr6-32471731-G-A
• rs2187823
• ENST00000449413.1:n.76+1694C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-32471731-G-A
• chr6-32471731-G-C
• chr6-32471731-G-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.88).
• 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

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.283

Alfa AF: 0.248 Hom.: 6049

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2187823; hg19: chr6-32439508;