6-33131433-A-G

Variant names:

• chr6-33131433-A-G
• rs2294472
• ENST00000454398.1:n.103-91T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_190905.1(LOC105375021):​n.493-91T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,010 control chromosomes in the GnomAD database, including 12,593 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 0.39 (12590 hom., cov: 31)
  • Exomes 𝑓: 0.43 (3 hom.)
• Consequence: LOC105375021 NR_190905.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449

Genes affected

HLA-DPA3 (HGNC:19393): (major histocompatibility complex, class II, DP alpha 3 (pseudogene))

LOC105375021 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375021	NR_190905.1	n.493-91T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DPA3	ENST00000454398.1	n.103-91T>C		intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59387 AN: 151862 Hom.: 12574 Cov.: 31

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.426

GnomAD4 exome AF: 0.429 AC: 12 AN: 28 Hom.: 3 AF XY: 0.571 AC XY: 8 AN XY: 14

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.400

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.391 AC: 59431 AN: 151982 Hom.: 12590 Cov.: 31 AF XY: 0.396 AC XY: 29408 AN XY: 74270

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.431

Alfa AF: 0.408 Hom.: 24376

Bravo AF: 0.400

Asia WGS AF: 0.558 AC: 1942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2294472; hg19: chr6-33099210;