Variant rs11771 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_006520.3(DYNLT3):c.183C>T(p.Ala61=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 1,169,836 control chromosomes in the GnomAD database, including 19,938 homozygotes. There are 69,861 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.31 ( 5606 hom., 9496 hem., cov: 22)

Exomes 𝑓: 0.18 ( 14332 hom. 60365 hem. )

Consequence

DYNLT3
NM_006520.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.608

Variant links:

Genes affected

DYNLT3 (HGNC:11694): (dynein light chain Tctex-type 3) This gene encodes a member of a subclass of dynein light chains. The encoded protein homodimerizes and forms the light chain component of the cytoplasmic dynein motor protein complex. This protein may be important for binding dynein to specific cargos including the spindle checkpoint protein BUB3. This protein may also function independently of dynein as a transcriptional modulator. Pseudogenes of this gene are found on chromosomes 2 and 20.[provided by RefSeq, Mar 2010]

DYNLT3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP6

Variant X-37841795-G-A is Benign according to our data. Variant chrX-37841795-G-A is described in ClinVar as [Benign]. Clinvar id is 402816.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-37841795-G-A is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-0.608 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DYNLT3	NM_006520.3 linkuse as main transcript	c.183C>T	p.Ala61=	synonymous_variant	3/5	ENST00000378578.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
DYNLT3	ENST00000378578.9 linkuse as main transcript	c.183C>T	p.Ala61=	synonymous_variant	3/5	1	NM_006520.3	P1
DYNLT3	ENST00000378581.7 linkuse as main transcript	c.183C>T	p.Ala61=	synonymous_variant	3/6	2
DYNLT3	ENST00000432389.2 linkuse as main transcript	c.201C>T	p.Ala67=	synonymous_variant	3/5	5

Frequencies

GnomAD3 genomes

AF:

0.308

AC:

33795

AN:

109893

Hom.:

5607

Cov.:

AF XY:

0.294

AC XY:

9461

AN XY:

32197

show subpopulations

Gnomad AFR

AF:

0.646

Gnomad AMI

AF:

0.164

Gnomad AMR

AF:

0.225

Gnomad ASJ

AF:

0.138

Gnomad EAS

AF:

0.226

Gnomad SAS

AF:

0.254

Gnomad FIN

AF:

0.188

Gnomad MID

AF:

0.214

Gnomad NFE

AF:

0.164

Gnomad OTH

AF:

0.264

GnomAD3 exomes

AF:

0.218

AC:

38439

AN:

176427

Hom.:

4048

AF XY:

0.202

AC XY:

12413

AN XY:

61335

show subpopulations

Gnomad AFR exome

AF:

0.660

Gnomad AMR exome

AF:

0.207

Gnomad ASJ exome

AF:

0.139

Gnomad EAS exome

AF:

0.229

Gnomad SAS exome

AF:

0.242

Gnomad FIN exome

AF:

0.193

Gnomad NFE exome

AF:

0.156

Gnomad OTH exome

AF:

0.197

GnomAD4 exome

AF:

0.178

AC:

188160

AN:

1059891

Hom.:

14332

Cov.:

AF XY:

0.178

AC XY:

60365

AN XY:

338771

show subpopulations

Gnomad4 AFR exome

AF:

0.659

Gnomad4 AMR exome

AF:

0.211

Gnomad4 ASJ exome

AF:

0.145

Gnomad4 EAS exome

AF:

0.269

Gnomad4 SAS exome

AF:

0.248

Gnomad4 FIN exome

AF:

0.192

Gnomad4 NFE exome

AF:

0.152

Gnomad4 OTH exome

AF:

0.195

GnomAD4 genome

AF:

0.308

AC:

33827

AN:

109945

Hom.:

5606

Cov.:

AF XY:

0.294

AC XY:

9496

AN XY:

32259

show subpopulations

Gnomad4 AFR

AF:

0.646

Gnomad4 AMR

AF:

0.225

Gnomad4 ASJ

AF:

0.138

Gnomad4 EAS

AF:

0.227

Gnomad4 SAS

AF:

0.257

Gnomad4 FIN

AF:

0.188

Gnomad4 NFE

AF:

0.164

Gnomad4 OTH

AF:

0.260

Alfa

AF:

0.231

Hom.:

2182

Bravo

AF:

0.327

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

4.1

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over