Genetic Variant DYNLRB1:c.79+355A>G (chr20-34526698-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 NM_014183.4(DYNLRB1):c.79+355A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 256,214 control chromosomes in the GnomAD database, including 28,480 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 0.47 ( 16793 hom., cov: 30)

Exomes 𝑓: 0.47 ( 11687 hom. )

Consequence

DYNLRB1
NM_014183.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.384

Publications

12 publications found

Variant links:

Genes affected

DYNLRB1 (HGNC:15468): (dynein light chain roadblock-type 1) This gene is a member of the roadblock dynein light chain family. The encoded cytoplasmic protein is capable of binding intermediate chain proteins, interacts with transforming growth factor-beta, and has been implicated in the regulation of actin modulating proteins. Upregulation of this gene has been associated with hepatocellular carcinomas, suggesting that this gene may be involved in tumor progression. Alternative splicing results in multiple transcript variants. Pseudogenes of this gene have been defined on chromosomes 12 and 18. [provided by RefSeq, Aug 2013]

DYNLRB1 links:

ENSG00000289720 (HGNC:):

ENSG00000289720 links:

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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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DYNLRB1	NM_014183.4 link	c.79+355A>G		intron_variant	Intron 2 of 3	ENST00000357156.7	NP_054902.1	Q9NP97-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DYNLRB1	ENST00000357156.7 link	c.79+355A>G		intron_variant	Intron 2 of 3	1	NM_014183.4	ENSP00000349679.2		Q9NP97-1
ENSG00000289720	ENST00000696979.1 link	n.*186+355A>G		intron_variant	Intron 26 of 27			ENSP00000513014.1

Frequencies

GnomAD3 genomes

AF:

0.465

AC:

70521

AN:

151656

Hom.:

16775

Cov.:

show subpopulations

Gnomad AFR

AF:

0.412

Gnomad AMI

AF:

0.420

Gnomad AMR

AF:

0.367

Gnomad ASJ

AF:

0.593

Gnomad EAS

AF:

0.394

Gnomad SAS

AF:

0.429

Gnomad FIN

AF:

0.590

Gnomad MID

AF:

0.503

Gnomad NFE

AF:

0.501

Gnomad OTH

AF:

0.475

GnomAD4 exome

AF:

0.472

AC:

49252

AN:

104440

Hom.:

11687

AF XY:

0.468

AC XY:

25383

AN XY:

54184

show subpopulations

African (AFR)

AF:

0.396

AC:

1749

AN:

4418

American (AMR)

AF:

0.318

AC:

1753

AN:

5506

Ashkenazi Jewish (ASJ)

AF:

0.596

AC:

1887

AN:

3166

East Asian (EAS)

AF:

0.371

AC:

2824

AN:

7622

South Asian (SAS)

AF:

0.430

AC:

4223

AN:

9820

European-Finnish (FIN)

AF:

0.576

AC:

2254

AN:

3912

Middle Eastern (MID)

AF:

0.549

AC:

223

AN:

406

European-Non Finnish (NFE)

AF:

0.494

AC:

31332

AN:

63438

Other (OTH)

AF:

0.489

AC:

3007

AN:

6152

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

1220

2440

3661

4881

6101

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

266

532

798

1064

1330

<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:

0.465

AC:

70576

AN:

151774

Hom.:

16793

Cov.:

AF XY:

0.468

AC XY:

34675

AN XY:

74160

show subpopulations

African (AFR)

AF:

0.412

AC:

17056

AN:

41348

American (AMR)

AF:

0.366

AC:

5589

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.593

AC:

2054

AN:

3466

East Asian (EAS)

AF:

0.393

AC:

2023

AN:

5150

South Asian (SAS)

AF:

0.430

AC:

2066

AN:

4810

European-Finnish (FIN)

AF:

0.590

AC:

6194

AN:

10494

Middle Eastern (MID)

AF:

0.500

AC:

147

AN:

294

European-Non Finnish (NFE)

AF:

0.501

AC:

34060

AN:

67934

Other (OTH)

AF:

0.477

AC:

1005

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1862

3723

5585

7446

9308

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

654

1308

1962

2616

3270

<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:

0.464

Hom.:

4944

Bravo

AF:

0.447

Asia WGS

AF:

0.428

AC:

1488

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.44

(source)

DANN

Benign

0.63

PhyloP100

-0.38

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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