rs2395357

Positions:

• chr6-33133229-G-A
• chr6-33133229-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000454398.1(HLA-DPA3):​n.103-1887C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.034 in 152,220 control chromosomes in the GnomAD database, including 152 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 0.034 (152 hom., cov: 32)
• Consequence: HLA-DPA3 ENST00000454398.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

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=-0.85).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.034 (5173/152220) while in subpopulation SAS AF= 0.0537 (258/4808). AF 95% confidence interval is 0.0483. There are 152 homozygotes in gnomad4. There are 2470 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 152 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375021	XR_926703.3	n.564+851C>T		intron_variant, non_coding_transcript_variant
LOC105375021	XR_001744086.2	n.564+851C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLA-DPA3	ENST00000454398.1	n.103-1887C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0340 AC: 5171 AN: 152102 Hom.: 153 Cov.: 32

Gnomad AFR AF: 0.00927

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0337

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.0538

Gnomad FIN AF: 0.0259

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0443

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0340 AC: 5173 AN: 152220 Hom.: 152 Cov.: 32 AF XY: 0.0332 AC XY: 2470 AN XY: 74436

Gnomad4 AFR AF: 0.00944

Gnomad4 AMR AF: 0.0336

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.0178

Gnomad4 SAS AF: 0.0537

Gnomad4 FIN AF: 0.0259

Gnomad4 NFE AF: 0.0443

Gnomad4 OTH AF: 0.0421

Alfa AF: 0.0254 Hom.: 20

Bravo AF: 0.0318

Asia WGS AF: 0.0390 AC: 136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.9
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: rs2395357; hg19: chr6-33101006;