Genetic Variant ENSG00000291111:n.553C>T (chr6-33118472-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000435074.7(ENSG00000291111):n.553C>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 0.354 in 155,312 control chromosomes in the GnomAD database, including 10,705 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 0.35 ( 10249 hom., cov: 31)

Exomes 𝑓: 0.46 ( 456 hom. )

Consequence

ENSG00000291111
ENST00000435074.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.80

Publications

31 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:

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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DPB2	NR_001435.2 link	n.364+1252C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000291111	ENST00000435074.7 link	n.553C>T	non_coding_transcript_exon_variant	Exon 3 of 3	6
ENSG00000291111	ENST00000684891.3 link	n.432C>T	non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000291111	ENST00000686632.2 link	n.427C>T	non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.352

AC:

53151

AN:

151178

Hom.:

10250

Cov.:

show subpopulations

Gnomad AFR

AF:

0.201

Gnomad AMI

AF:

0.430

Gnomad AMR

AF:

0.290

Gnomad ASJ

AF:

0.571

Gnomad EAS

AF:

0.379

Gnomad SAS

AF:

0.551

Gnomad FIN

AF:

0.407

Gnomad MID

AF:

0.490

Gnomad NFE

AF:

0.419

Gnomad OTH

AF:

0.359

GnomAD2 exomes

AF:

0.421

AC:

2702

AN:

6418

AF XY:

0.438

show subpopulations

Gnomad AFR exome

AF:

0.158

Gnomad AMR exome

AF:

0.254

Gnomad ASJ exome

AF:

0.599

Gnomad EAS exome

AF:

0.287

Gnomad FIN exome

AF:

0.333

Gnomad NFE exome

AF:

0.435

Gnomad OTH exome

AF:

0.420

GnomAD4 exome

AF:

0.459

AC:

1844

AN:

4014

Hom.:

456

Cov.:

AF XY:

0.453

AC XY:

1090

AN XY:

2404

show subpopulations

African (AFR)

AF:

0.163

AC:

AN:

American (AMR)

AF:

0.182

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.538

AC:

AN:

East Asian (EAS)

AF:

0.333

AC:

AN:

South Asian (SAS)

AF:

0.519

AC:

196

AN:

378

European-Finnish (FIN)

AF:

0.388

AC:

186

AN:

480

Middle Eastern (MID)

AF:

0.531

AC:

868

AN:

1636

European-Non Finnish (NFE)

AF:

0.399

AC:

416

AN:

1042

Other (OTH)

AF:

0.453

AC:

126

AN:

278

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

142

189

236

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

110

<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:

0.351

AC:

53162

AN:

151298

Hom.:

10249

Cov.:

AF XY:

0.354

AC XY:

26165

AN XY:

73928

show subpopulations

African (AFR)

AF:

0.201

AC:

8257

AN:

41122

American (AMR)

AF:

0.290

AC:

4409

AN:

15200

Ashkenazi Jewish (ASJ)

AF:

0.571

AC:

1976

AN:

3460

East Asian (EAS)

AF:

0.378

AC:

1931

AN:

5112

South Asian (SAS)

AF:

0.551

AC:

2644

AN:

4798

European-Finnish (FIN)

AF:

0.407

AC:

4272

AN:

10500

Middle Eastern (MID)

AF:

0.490

AC:

142

AN:

290

European-Non Finnish (NFE)

AF:

0.419

AC:

28390

AN:

67800

Other (OTH)

AF:

0.356

AC:

750

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1646

3291

4937

6582

8228

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

532

1064

1596

2128

2660

<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:

0.398

Hom.:

24486

Bravo

AF:

0.329

Asia WGS

AF:

0.445

AC:

1549

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.7

(source)

DANN

Benign

0.52

PhyloP100

-1.8

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