ENST00000783029.1:n.443C>T

Variant names:

• chr6-33139684-G-A
• rs4711319
• ENST00000783029.1:n.443C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000783029.1(ENSG00000301948):​n.443C>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: ENSG00000301948 ENST00000783029.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 17 publications found

Genes affected

ENSG00000301948 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105375021	NR_190905.1	n.277C>T		non_coding_transcript_exon_variant	Exon 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301948	ENST00000783029.1	n.443C>T		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000301948	ENST00000783030.1	n.443C>T		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000301948	ENST00000783031.1	n.443C>T		non_coding_transcript_exon_variant	Exon 2 of 5

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

African (AFR) AF: 0.0553 AC: 2293 AN: 41500

American (AMR) AF: 0.150 AC: 2297 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 918 AN: 3470

East Asian (EAS) AF: 0.255 AC: 1317 AN: 5168

South Asian (SAS) AF: 0.169 AC: 813 AN: 4818

European-Finnish (FIN) AF: 0.155 AC: 1644 AN: 10580

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10427 AN: 67998

Other (OTH) AF: 0.145 AC: 306 AN: 2114

Alfa AF: 0.140 Hom.: 2309

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
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs4711319; hg19: chr6-33107461;