Genetic Variant ENST00000539757.1:n.184-1163T>C (chr12-9287039-T-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000539757.1(DDX12B):n.184-1163T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.27 ( 935 hom., cov: 17)

Failed GnomAD Quality Control

Consequence

DDX12B
ENST00000539757.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.459

Publications

1 publications found

Variant links:

Genes affected

DDX12B (HGNC:38668): (DEAD/H-box helicase 12B%2C pseudogene [Source:HGNC Symbol%3BAcc:HGNC:38668])

DDX12B links:

ENSG00000295087 (HGNC:):

ENSG00000295087 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC642846	NR_024374.1 link	n.241-1163T>C		intron_variant	Intron 1 of 21

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DDX12B	ENST00000539757.1 link	n.184-1163T>C	intron_variant	Intron 2 of 28	6
ENSG00000295087	ENST00000727879.1 link	n.255-1163T>C	intron_variant	Intron 1 of 7
ENSG00000295087	ENST00000727880.1 link	n.174-1163T>C	intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes

AF:

0.266

AC:

25467

AN:

95618

Hom.:

927

Cov.:

show subpopulations

Gnomad AFR

AF:

0.264

Gnomad AMI

AF:

0.306

Gnomad AMR

AF:

0.276

Gnomad ASJ

AF:

0.335

Gnomad EAS

AF:

0.180

Gnomad SAS

AF:

0.331

Gnomad FIN

AF:

0.307

Gnomad MID

AF:

0.315

Gnomad NFE

AF:

0.259

Gnomad OTH

AF:

0.263

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

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.266

AC:

25498

AN:

95684

Hom.:

935

Cov.:

AF XY:

0.265

AC XY:

12086

AN XY:

45648

show subpopulations

African (AFR)

AF:

0.265

AC:

6278

AN:

23702

American (AMR)

AF:

0.276

AC:

2703

AN:

9792

Ashkenazi Jewish (ASJ)

AF:

0.335

AC:

735

AN:

2194

East Asian (EAS)

AF:

0.180

AC:

692

AN:

3848

South Asian (SAS)

AF:

0.333

AC:

826

AN:

2484

European-Finnish (FIN)

AF:

0.307

AC:

1948

AN:

6352

Middle Eastern (MID)

AF:

0.300

AC:

AN:

220

European-Non Finnish (NFE)

AF:

0.259

AC:

11705

AN:

45108

Other (OTH)

AF:

0.260

AC:

350

AN:

1346

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.413

Heterozygous variant carriers

1219

2437

3656

4874

6093

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

278

556

834

1112

1390

<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:

0.191

Hom.:

120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.1

(source)

DANN

Benign

0.27

PhyloP100

-0.46

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over