rs9268831

Variant names:

• chr6-32459971-C-A
• rs9268831
• ENST00000449413.1:n.193G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-32459971-C-A
• chr6-32459971-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000449413.1(HLA-DRB9):​n.193G>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.00000272 in 367,686 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: HLA-DRB9 ENST00000449413.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.97
• Publications: 54 publications found

Genes affected

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

ENSG00000299747 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DRB9		n.32459971C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DRB9	ENST00000449413.1	n.193G>T		non_coding_transcript_exon_variant	Exon 2 of 2	6
ENSG00000299747	ENST00000766007.1	n.11G>T		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000299747	ENST00000766008.1	n.14G>T		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000299747	ENST00000766009.1	n.376G>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000272 AC: 1 AN: 367686 Hom.: 0 Cov.: 0 AF XY: 0.00000474 AC XY: 1 AN XY: 210772

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 10510

American (AMR) AF: 0.00 AC: 0 AN: 36300

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11744

East Asian (EAS) AF: 0.00 AC: 0 AN: 13170

South Asian (SAS) AF: 0.0000149 AC: 1 AN: 67178

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 17474

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2852

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 191844

Other (OTH) AF: 0.00 AC: 0 AN: 16614

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	12
DANN	Benign	0.62
PhyloP100		4.0

Splicing

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

Other links and lift over

dbSNP: rs9268831; hg19: chr6-32427748;