Variant rs3802427 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007234.5(DCTN3):c.181+32G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 1,569,298 control chromosomes in the GnomAD database, including 25,640 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 0.18 ( 2555 hom., cov: 32)

Exomes 𝑓: 0.18 ( 23085 hom. )

Consequence

DCTN3
NM_007234.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.290

Variant links:

Genes affected

DCTN3 (HGNC:2713): (dynactin subunit 3) This gene encodes the smallest subunit of dynactin, a macromolecular complex consisting of 10 subunits ranging in size from 22 to 150 kD. Dynactin binds to both microtubules and cytoplasmic dynein. It is involved in a diverse array of cellular functions, including ER-to-Golgi transport, the centripetal movement of lysosomes and endosomes, spindle formation, cytokinesis, chromosome movement, nuclear positioning, and axonogenesis. This subunit, like most other dynactin subunits, exists only as a part of the dynactin complex. It is primarily an alpha-helical protein with very little coiled coil, and binds directly to the largest subunit (p150) of dynactin. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

DCTN3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCTN3	NM_007234.5 link	c.181+32G>A		intron_variant		ENST00000259632.12	NP_009165.1	O75935-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCTN3	ENST00000259632.12 link	c.181+32G>A		intron_variant		1	NM_007234.5	ENSP00000259632.7		O75935-1

Frequencies

GnomAD3 genomes

AF:

0.182

AC:

27650

AN:

151982

Hom.:

2557

Cov.:

show subpopulations

Gnomad AFR

AF:

0.196

Gnomad AMI

AF:

0.240

Gnomad AMR

AF:

0.225

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.307

Gnomad SAS

AF:

0.197

Gnomad FIN

AF:

0.132

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.163

Gnomad OTH

AF:

0.190

GnomAD3 exomes

AF:

0.195

AC:

49068

AN:

251018

Hom.:

5328

AF XY:

0.191

AC XY:

25928

AN XY:

135712

show subpopulations

Gnomad AFR exome

AF:

0.198

Gnomad AMR exome

AF:

0.287

Gnomad ASJ exome

AF:

0.120

Gnomad EAS exome

AF:

0.318

Gnomad SAS exome

AF:

0.201

Gnomad FIN exome

AF:

0.140

Gnomad NFE exome

AF:

0.165

Gnomad OTH exome

AF:

0.171

GnomAD4 exome

AF:

0.175

AC:

248694

AN:

1417198

Hom.:

23085

Cov.:

AF XY:

0.175

AC XY:

124187

AN XY:

707658

show subpopulations

Gnomad4 AFR exome

AF:

0.198

Gnomad4 AMR exome

AF:

0.279

Gnomad4 ASJ exome

AF:

0.117

Gnomad4 EAS exome

AF:

0.311

Gnomad4 SAS exome

AF:

0.201

Gnomad4 FIN exome

AF:

0.136

Gnomad4 NFE exome

AF:

0.167

Gnomad4 OTH exome

AF:

0.171

GnomAD4 genome

AF:

0.182

AC:

27655

AN:

152100

Hom.:

2555

Cov.:

AF XY:

0.182

AC XY:

13544

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.196

Gnomad4 AMR

AF:

0.226

Gnomad4 ASJ

AF:

0.117

Gnomad4 EAS

AF:

0.307

Gnomad4 SAS

AF:

0.196

Gnomad4 FIN

AF:

0.132

Gnomad4 NFE

AF:

0.163

Gnomad4 OTH

AF:

0.188

Alfa

AF:

0.165

Hom.:

1137

Bravo

AF:

0.193

Asia WGS

AF:

0.258

AC:

900

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.82

DANN

Benign

0.31

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over