rs3828840

Variant names:

• chr6-32553130-T-A
• rs3828840
• ENST00000411500.5:n.876-58A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-32553130-T-A
• chr6-32553130-T-C
• chr6-32553130-T-G

Variant summary

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

The ENST00000411500.5(HLA-DRB6):​n.876-58A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 27)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HLA-DRB6 ENST00000411500.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32
• Publications: 28 publications found

Genes affected

HLA-DRB6 (HGNC:):

HLA-DRB6 (HGNC:4954): (major histocompatibility complex, class II, DR beta 6 (pseudogene))

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=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DRB6	NR_001298.1	n.876-58A>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DRB6	ENST00000411500.5	n.876-58A>T		intron_variant	Intron 5 of 5	6
HLA-DRB6	ENST00000437183.5	n.967-58A>T		intron_variant	Intron 5 of 5	6
HLA-DRB6	ENST00000437650.2	n.689-58A>T		intron_variant	Intron 4 of 4	6
HLA-DRB6	ENST00000804227.1	n.949-58A>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 315368 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 176372

African (AFR) AF: 0.00 AC: 0 AN: 6844

American (AMR) AF: 0.00 AC: 0 AN: 21080

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9054

East Asian (EAS) AF: 0.00 AC: 0 AN: 14850

South Asian (SAS) AF: 0.00 AC: 0 AN: 43498

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28294

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2102

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 174268

Other (OTH) AF: 0.00 AC: 0 AN: 15378

GnomAD4 genome Cov.: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.32
DANN	Benign	0.36
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs3828840; hg19: chr6-32520907;