Genetic Variant ENST00000471626.1:n.349-139C>T (chr3-128470729-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 ENST00000471626.1(DNAJB8-AS1):n.349-139C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 152,262 control chromosomes in the GnomAD database, including 20,444 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 0.50 ( 20433 hom., cov: 33)

Exomes 𝑓: 0.44 ( 11 hom. )

Consequence

DNAJB8-AS1
ENST00000471626.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.29

Publications

5 publications found

Variant links:

Genes affected

DNAJB8-AS1 (HGNC:41029): (DNAJB8 antisense RNA 1)

DNAJB8-AS1 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000471626.1. 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
	DNAJB8-AS1	NR_037890.1		n.349-139C>T		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
DNAJB8-AS1	ENST00000471626.1	TSL:2	n.349-139C>T	intron	N/A
DNAJB8-AS1	ENST00000746121.1		n.353-2246C>T	intron	N/A
DNAJB8-AS1	ENST00000746122.1		n.199-2246C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.500

AC:

76040

AN:

152048

Hom.:

20404

Cov.:

show subpopulations

Gnomad AFR

AF:

0.697

Gnomad AMI

AF:

0.297

Gnomad AMR

AF:

0.432

Gnomad ASJ

AF:

0.414

Gnomad EAS

AF:

0.561

Gnomad SAS

AF:

0.582

Gnomad FIN

AF:

0.357

Gnomad MID

AF:

0.519

Gnomad NFE

AF:

0.415

Gnomad OTH

AF:

0.486

GnomAD4 exome

AF:

0.436

AC:

AN:

Hom.:

AF XY:

0.456

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.372

AC:

AN:

Other (OTH)

AF:

0.750

AC:

AN:

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

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:

0.500

AC:

76130

AN:

152168

Hom.:

20433

Cov.:

AF XY:

0.497

AC XY:

36993

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.697

AC:

28923

AN:

41504

American (AMR)

AF:

0.431

AC:

6597

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.414

AC:

1437

AN:

3472

East Asian (EAS)

AF:

0.562

AC:

2907

AN:

5176

South Asian (SAS)

AF:

0.583

AC:

2813

AN:

4824

European-Finnish (FIN)

AF:

0.357

AC:

3780

AN:

10600

Middle Eastern (MID)

AF:

0.524

AC:

154

AN:

294

European-Non Finnish (NFE)

AF:

0.415

AC:

28214

AN:

67980

Other (OTH)

AF:

0.489

AC:

1034

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1855

3710

5566

7421

9276

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

664

1328

1992

2656

3320

<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:

0.435

Hom.:

29904

Bravo

AF:

0.513

Asia WGS

AF:

0.542

AC:

1886

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.54

(source)

DANN

Benign

0.35

PhyloP100

-1.3

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over