Variant 3-196296090-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_152773.5(DYNLT2B):c.318-21C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0515 in 1,608,362 control chromosomes in the GnomAD database, including 2,444 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.040 ( 159 hom., cov: 33)

Exomes 𝑓: 0.053 ( 2285 hom. )

Consequence

DYNLT2B
NM_152773.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.00700

Variant links:

Genes affected

DYNLT2B (HGNC:28482): (dynein light chain Tctex-type 2B) Dyneins are a group of microtubule-activated ATPases that function as molecular motors. They are divided into two subgroups of axonemal and cytoplasmic dyneins. The cytoplasmic dyneins function in intracellular motility, including retrograde axonal transport, protein sorting, organelle movement, and spindle dynamics. Molecules of conventional cytoplasmic dynein are comprised of 2 heavy chain polypeptides and a number of intermediate and light chains. This gene encodes a subunit of the human cytoplasmic dynein-2 complex. Mutations in this gene are associated with short-rib thoracic dysplasia 17 with or without polydactyly. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2017]

DYNLT2B links:

ENSG00000272741 (HGNC:):

ENSG00000272741 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 3-196296090-G-T is Benign according to our data. Variant chr3-196296090-G-T is described in ClinVar as [Benign]. Clinvar id is 1279376.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DYNLT2B	NM_152773.5 linkuse as main transcript	c.318-21C>A		intron_variant		ENST00000325318.10	NP_689986.2
DYNLT2B	NM_001351628.2 linkuse as main transcript	c.318-21C>A		intron_variant			NP_001338557.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DYNLT2B	ENST00000325318.10 linkuse as main transcript	c.318-21C>A		intron_variant		1	NM_152773.5	ENSP00000324323.5		Q8WW35
ENSG00000272741	ENST00000431391.1 linkuse as main transcript	n.317+10853C>A		intron_variant		5		ENSP00000405181.1		E7ESA3

Frequencies

GnomAD3 genomes

AF:

0.0401

AC:

6105

AN:

152064

Hom.:

159

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0201

Gnomad AMI

AF:

0.0461

Gnomad AMR

AF:

0.0321

Gnomad ASJ

AF:

0.0505

Gnomad EAS

AF:

0.0782

Gnomad SAS

AF:

0.0320

Gnomad FIN

AF:

0.0422

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0510

Gnomad OTH

AF:

0.0374

GnomAD3 exomes

AF:

0.0460

AC:

11541

AN:

251068

Hom.:

315

AF XY:

0.0471

AC XY:

6396

AN XY:

135704

show subpopulations

Gnomad AFR exome

AF:

0.0187

Gnomad AMR exome

AF:

0.0209

Gnomad ASJ exome

AF:

0.0548

Gnomad EAS exome

AF:

0.0694

Gnomad SAS exome

AF:

0.0389

Gnomad FIN exome

AF:

0.0484

Gnomad NFE exome

AF:

0.0542

Gnomad OTH exome

AF:

0.0487

GnomAD4 exome

AF:

0.0527

AC:

76740

AN:

1456180

Hom.:

2285

Cov.:

AF XY:

0.0522

AC XY:

37863

AN XY:

724778

show subpopulations

Gnomad4 AFR exome

AF:

0.0183

Gnomad4 AMR exome

AF:

0.0219

Gnomad4 ASJ exome

AF:

0.0537

Gnomad4 EAS exome

AF:

0.0872

Gnomad4 SAS exome

AF:

0.0377

Gnomad4 FIN exome

AF:

0.0523

Gnomad4 NFE exome

AF:

0.0550

Gnomad4 OTH exome

AF:

0.0515

GnomAD4 genome

AF:

0.0401

AC:

6104

AN:

152182

Hom.:

159

Cov.:

AF XY:

0.0387

AC XY:

2881

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.0200

Gnomad4 AMR

AF:

0.0320

Gnomad4 ASJ

AF:

0.0505

Gnomad4 EAS

AF:

0.0780

Gnomad4 SAS

AF:

0.0322

Gnomad4 FIN

AF:

0.0422

Gnomad4 NFE

AF:

0.0510

Gnomad4 OTH

AF:

0.0384

Alfa

AF:

0.0367

Hom.:

Bravo

AF:

0.0386

Asia WGS

AF:

0.0660

AC:

229

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 19, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.5

DANN

Benign

0.72

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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