Variant rs3816989 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_152665.3(DYNLT5):c.336+1G>A variant causes a splice donor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.134 in 1,596,222 control chromosomes in the GnomAD database, including 14,913 homozygotes. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.12 ( 1139 hom., cov: 32)

Exomes 𝑓: 0.14 ( 13774 hom. )

Consequence

DYNLT5
NM_152665.3 splice_donor, intron

Scores

Splicing: ADA: 1.000

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 8.33

Variant links:

Genes affected

DYNLT5 (HGNC:26882): (dynein light chain Tctex-type family member 5) Predicted to enable dynein intermediate chain binding activity. Predicted to be involved in microtubule-based movement. Predicted to be part of cytoplasmic dynein complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

DYNLT5 links:

DYNLT5 (HGNC:):

DYNLT5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DYNLT5	NM_152665.3 linkuse as main transcript	c.336+1G>A		splice_donor_variant, intron_variant		ENST00000282670.7	NP_689878.2	Q8N7M0-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
DYNLT5	ENST00000282670.7 linkuse as main transcript	c.336+1G>A	splice_donor_variant, intron_variant	1	NM_152665.3	ENSP00000282670.2	Q8N7M0-1
DYNLT5	ENST00000528352.1 linkuse as main transcript	n.*235+1G>A	splice_donor_variant, intron_variant	1		ENSP00000436731.1	E9PI84
DYNLT5	ENST00000489510.1 linkuse as main transcript	n.249+1G>A	splice_donor_variant, intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

17999

AN:

152006

Hom.:

1138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0820

Gnomad AMI

AF:

0.174

Gnomad AMR

AF:

0.112

Gnomad ASJ

AF:

0.176

Gnomad EAS

AF:

0.136

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.134

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.131

Gnomad OTH

AF:

0.126

GnomAD3 exomes

AF:

0.136

AC:

33160

AN:

244602

Hom.:

2428

AF XY:

0.142

AC XY:

18709

AN XY:

132080

show subpopulations

Gnomad AFR exome

AF:

0.0808

Gnomad AMR exome

AF:

0.0873

Gnomad ASJ exome

AF:

0.187

Gnomad EAS exome

AF:

0.143

Gnomad SAS exome

AF:

0.176

Gnomad FIN exome

AF:

0.138

Gnomad NFE exome

AF:

0.141

Gnomad OTH exome

AF:

0.137

GnomAD4 exome

AF:

0.136

AC:

195787

AN:

1444098

Hom.:

13774

Cov.:

AF XY:

0.137

AC XY:

98437

AN XY:

716292

show subpopulations

Gnomad4 AFR exome

AF:

0.0770

Gnomad4 AMR exome

AF:

0.0894

Gnomad4 ASJ exome

AF:

0.183

Gnomad4 EAS exome

AF:

0.149

Gnomad4 SAS exome

AF:

0.169

Gnomad4 FIN exome

AF:

0.134

Gnomad4 NFE exome

AF:

0.135

Gnomad4 OTH exome

AF:

0.138

GnomAD4 genome

AF:

0.118

AC:

17998

AN:

152124

Hom.:

1139

Cov.:

AF XY:

0.118

AC XY:

8753

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.0819

Gnomad4 AMR

AF:

0.112

Gnomad4 ASJ

AF:

0.176

Gnomad4 EAS

AF:

0.137

Gnomad4 SAS

AF:

0.160

Gnomad4 FIN

AF:

0.134

Gnomad4 NFE

AF:

0.131

Gnomad4 OTH

AF:

0.125

Alfa

AF:

0.134

Hom.:

2446

Bravo

AF:

0.117

TwinsUK

AF:

0.133

AC:

495

ALSPAC

AF:

0.121

AC:

468

ESP6500AA

AF:

0.0831

AC:

366

ESP6500EA

AF:

0.138

AC:

1187

ExAC

AF:

0.137

AC:

16572

Asia WGS

AF:

0.128

AC:

446

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Uncertain

0.015

BayesDel_noAF

Pathogenic

0.39

CADD

Pathogenic

DANN

Uncertain

1.0

Eigen

Pathogenic

1.2

Eigen_PC

Pathogenic

1.1

FATHMM_MKL

Pathogenic

0.99

GERP RS

5.9

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

1.0

dbscSNV1_RF

Pathogenic

0.94

SpliceAI score (max)

0.99

Details are displayed if max score is > 0.2

DS_DL_spliceai

0.99

Position offset: -1

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over