6-33134085-G-A

Variant names:

• chr6-33134085-G-A
• rs35410698
• ENST00000783029.1:n.725C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000783029.1(ENSG00000301948):​n.725C>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 0.0359 in 152,196 control chromosomes in the GnomAD database, including 169 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 0.036 (169 hom., cov: 32)
• Consequence: ENSG00000301948 ENST00000783029.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 4 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).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0359 (5463/152196) while in subpopulation SAS AF = 0.0537 (259/4822). AF 95% confidence interval is 0.0483. There are 169 homozygotes in GnomAd4. There are 2612 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 169 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375021	NR_190905.1	n.487C>T		non_coding_transcript_exon_variant	Exon 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301948	ENST00000783029.1	n.725C>T		non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000301948	ENST00000783030.1	n.653C>T		non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000301948	ENST00000783031.1	n.725C>T		non_coding_transcript_exon_variant	Exon 3 of 5

Frequencies

GnomAD3 genomes AF: 0.0359 AC: 5460 AN: 152078 Hom.: 170 Cov.: 32

Gnomad AFR AF: 0.0100

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.0379

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.0539

Gnomad FIN AF: 0.0261

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0465

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0359 AC: 5463 AN: 152196 Hom.: 169 Cov.: 32 AF XY: 0.0351 AC XY: 2612 AN XY: 74414

African (AFR) AF: 0.0102 AC: 424 AN: 41528

American (AMR) AF: 0.0378 AC: 578 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 539 AN: 3472

East Asian (EAS) AF: 0.0180 AC: 93 AN: 5180

South Asian (SAS) AF: 0.0537 AC: 259 AN: 4822

European-Finnish (FIN) AF: 0.0261 AC: 277 AN: 10602

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.0465 AC: 3163 AN: 67990

Other (OTH) AF: 0.0460 AC: 97 AN: 2110

Alfa AF: 0.0278 Hom.: 29

Bravo AF: 0.0340

Asia WGS AF: 0.0400 AC: 141 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	7.5
DANN	Benign	0.51
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs35410698; hg19: chr6-33101862;