Genetic Variant DYNLRB1:c.79+355A>T (chr20-34526698-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_014183.4(DYNLRB1):c.79+355A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

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: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

105146

Hom.:

AF XY:

0.00

AC XY:

AN XY:

54576

African (AFR)

AF:

0.00

AC:

AN:

4464

American (AMR)

AF:

0.00

AC:

AN:

5524

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3188

East Asian (EAS)

AF:

0.00

AC:

AN:

7674

South Asian (SAS)

AF:

0.00

AC:

AN:

9894

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3924

Middle Eastern (MID)

AF:

0.00

AC:

AN:

412

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

63860

Other (OTH)

AF:

0.00

AC:

AN:

6206

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

4944

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.32

(source)

DANN

Benign

0.78

PhyloP100

-0.38

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over