rs6087592

Positions:

• chr20-34526698-A-G
• chr20-34526698-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
DYNLRB1	NM_014183.4	c.79+355A>G		intron_variant		ENST00000357156.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DYNLRB1	ENST00000357156.7	c.79+355A>G		intron_variant		1	NM_014183.4	P1

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70521 AN: 151656 Hom.: 16775 Cov.: 30

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

Gnomad4 AFR exome AF: 0.396

Gnomad4 AMR exome AF: 0.318

Gnomad4 ASJ exome AF: 0.596

Gnomad4 EAS exome AF: 0.371

Gnomad4 SAS exome AF: 0.430

Gnomad4 FIN exome AF: 0.576

Gnomad4 NFE exome AF: 0.494

Gnomad4 OTH exome AF: 0.489

GnomAD4 genome AF: 0.465 AC: 70576 AN: 151774 Hom.: 16793 Cov.: 30 AF XY: 0.468 AC XY: 34675 AN XY: 74160

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.477

Alfa AF: 0.469 Hom.: 4437

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
DANN	Benign	0.63

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

LitVar

Other links and lift over

dbSNP: rs6087592; hg19: chr20-33114503;