Genetic Variant ENSG00000291111:n.430-9932C>A (chr6-33131189-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000782892.1(ENSG00000291111):n.430-9932C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 152,098 control chromosomes in the GnomAD database, including 17,024 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 0.46 ( 17009 hom., cov: 32)

Exomes 𝑓: 0.42 ( 15 hom. )

Consequence

ENSG00000291111
ENST00000782892.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.430

Publications

30 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375021	NR_190905.1 link	n.638+8G>T		splice_region_variant, intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000291111	ENST00000782892.1 link	n.430-9932C>A	intron_variant	Intron 2 of 2
ENSG00000291111	ENST00000782893.1 link	n.404-9932C>A	intron_variant	Intron 2 of 2
ENSG00000291111	ENST00000782894.1 link	n.229-56C>A	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.457

AC:

69359

AN:

151836

Hom.:

16996

Cov.:

show subpopulations

Gnomad AFR

AF:

0.296

Gnomad AMI

AF:

0.491

Gnomad AMR

AF:

0.572

Gnomad ASJ

AF:

0.642

Gnomad EAS

AF:

0.771

Gnomad SAS

AF:

0.588

Gnomad FIN

AF:

0.480

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.480

Gnomad OTH

AF:

0.493

GnomAD4 exome

AF:

0.424

AC:

AN:

144

Hom.:

Cov.:

AF XY:

0.429

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.625

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.667

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.440

AC:

AN:

100

Other (OTH)

AF:

0.143

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.457

AC:

69403

AN:

151954

Hom.:

17009

Cov.:

AF XY:

0.463

AC XY:

34407

AN XY:

74280

show subpopulations

African (AFR)

AF:

0.296

AC:

12259

AN:

41422

American (AMR)

AF:

0.572

AC:

8739

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.642

AC:

2229

AN:

3470

East Asian (EAS)

AF:

0.772

AC:

3968

AN:

5140

South Asian (SAS)

AF:

0.590

AC:

2838

AN:

4810

European-Finnish (FIN)

AF:

0.480

AC:

5072

AN:

10556

Middle Eastern (MID)

AF:

0.650

AC:

191

AN:

294

European-Non Finnish (NFE)

AF:

0.480

AC:

32613

AN:

67968

Other (OTH)

AF:

0.497

AC:

1048

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1813

3625

5438

7250

9063

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

636

1272

1908

2544

3180

<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:

0.477

Hom.:

51731

Bravo

AF:

0.459

Asia WGS

AF:

0.616

AC:

2142

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.4

(source)

DANN

Benign

0.77

PhyloP100

-0.43

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