dbSNP rs3117004: ENSG00000291111:n.1381A>C (chr6-33128989-A-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000782902.1(ENSG00000291111):n.1381A>C 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 0.0000128 in 234,418 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)

Exomes 𝑓: 0.000013 ( 0 hom. )

Consequence

ENSG00000291111
ENST00000782902.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Publications

0 publications found

Variant links:

Genes affected

ENSG00000291111 (HGNC:):

ENSG00000291111 links:

HLA-DPB2 (HGNC:4941): (major histocompatibility complex, class II, DP beta 2 (pseudogene))

HLA-DPB2 links:

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new If you want to explore the variant's impact on the transcript ENST00000782902.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782902.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DPB2	NR_001435.2		n.757-76A>C		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ENSG00000291111	ENST00000782902.1		n.1381A>C	non_coding_transcript_exon	Exon 2 of 2
HLA-DPB2	ENST00000470997.1	TSL:6	n.757-76A>C	intron	N/A
ENSG00000291111	ENST00000782892.1		n.429+11769A>C	intron	N/A

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.0000128

AC:

AN:

234418

Hom.:

AF XY:

0.0000220

AC XY:

AN XY:

136300

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

5682

American (AMR)

AF:

0.00

AC:

AN:

23348

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

6516

East Asian (EAS)

AF:

0.00

AC:

AN:

7044

South Asian (SAS)

AF:

0.0000729

AC:

AN:

41164

European-Finnish (FIN)

AF:

0.00

AC:

AN:

18508

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2400

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

119018

Other (OTH)

AF:

0.00

AC:

AN:

10738

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.4

(source)

DANN

Benign

0.38

PhyloP100

-1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over