Genetic Variant ENSG00000291111:n.457A>G (chr6-33131433-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000782900.1(ENSG00000291111):n.457A>G 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 0.391 in 152,010 control chromosomes in the GnomAD database, including 12,593 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 0.39 ( 12590 hom., cov: 31)

Exomes 𝑓: 0.43 ( 3 hom. )

Consequence

ENSG00000291111
ENST00000782900.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.449

Publications

27 publications found

Variant links:

Genes affected

ENSG00000291111 (HGNC:):

ENSG00000291111 links:

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

HLA-DPA3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375021	NR_190905.1 link	n.493-91T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000291111	ENST00000782900.1 link	n.457A>G	non_coding_transcript_exon_variant	Exon 3 of 3
HLA-DPA3	ENST00000454398.1 link	n.103-91T>C	intron_variant	Intron 1 of 1	6
ENSG00000291111	ENST00000782892.1 link	n.430-9688A>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.391

AC:

59387

AN:

151862

Hom.:

12574

Cov.:

show subpopulations

Gnomad AFR

AF:

0.284

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.521

Gnomad ASJ

AF:

0.551

Gnomad EAS

AF:

0.762

Gnomad SAS

AF:

0.422

Gnomad FIN

AF:

0.407

Gnomad MID

AF:

0.503

Gnomad NFE

AF:

0.387

Gnomad OTH

AF:

0.426

GnomAD4 exome

AF:

0.429

AC:

AN:

Hom.:

AF XY:

0.571

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.400

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.542

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.391

AC:

59431

AN:

151982

Hom.:

12590

Cov.:

AF XY:

0.396

AC XY:

29408

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.284

AC:

11754

AN:

41440

American (AMR)

AF:

0.521

AC:

7955

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.551

AC:

1913

AN:

3470

East Asian (EAS)

AF:

0.762

AC:

3942

AN:

5172

South Asian (SAS)

AF:

0.423

AC:

2036

AN:

4812

European-Finnish (FIN)

AF:

0.407

AC:

4286

AN:

10536

Middle Eastern (MID)

AF:

0.483

AC:

142

AN:

294

European-Non Finnish (NFE)

AF:

0.387

AC:

26274

AN:

67960

Other (OTH)

AF:

0.431

AC:

907

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1728

3457

5185

6914

8642

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

562

1124

1686

2248

2810

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.402

Hom.:

56178

Bravo

AF:

0.400

Asia WGS

AF:

0.558

AC:

1942

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.7

(source)

DANN

Benign

0.54

PhyloP100

-0.45

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over