rs4711319

chr6-33139684-G-A

Variant summary

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

The XR_926703.3(LOC105375021):n.277C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,142 control chromosomes in the GnomAD database, including 1,601 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 0.13 (1601 hom., cov: 33)
• Consequence: LOC105375021 XR_926703.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

Genes affected

LOC105375021 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375021	XR_926703.3	n.277C>T		non_coding_transcript_exon_variant	2/4
LOC105375021	XR_001744086.2	n.277C>T		non_coding_transcript_exon_variant	2/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-DPA3	ENST00000454398.1	n.102+3540C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20188 AN: 152024 Hom.: 1603 Cov.: 33

Gnomad AFR AF: 0.0554

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.133 AC: 20180 AN: 152142 Hom.: 1601 Cov.: 33 AF XY: 0.134 AC XY: 9977 AN XY: 74372

Gnomad4 AFR AF: 0.0553

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.145

Alfa AF: 0.155 Hom.: 972

Bravo AF: 0.130

Asia WGS AF: 0.209 AC: 728 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	1.6
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4711319; hg19: chr6-33107461;