Variant chr3-196296136-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_152773.5(DYNLT2B):c.318-67G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0654 in 1,323,530 control chromosomes in the GnomAD database, including 3,369 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.065 ( 380 hom., cov: 32)

Exomes 𝑓: 0.065 ( 2989 hom. )

Consequence

DYNLT2B
NM_152773.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.37

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP6

Variant 3-196296136-C-T is Benign according to our data. Variant chr3-196296136-C-T is described in ClinVar as [Benign]. Clinvar id is 1262426.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DYNLT2B	NM_152773.5 linkuse as main transcript	c.318-67G>A		intron_variant		ENST00000325318.10
DYNLT2B	NM_001351628.2 linkuse as main transcript	c.318-67G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
DYNLT2B	ENST00000325318.10 linkuse as main transcript	c.318-67G>A	intron_variant		1	NM_152773.5	P1
DYNLT2B	ENST00000465757.5 linkuse as main transcript	n.171G>A	non_coding_transcript_exon_variant	1/2	2
DYNLT2B	ENST00000426563.5 linkuse as main transcript	c.*184-67G>A	intron_variant, NMD_transcript_variant		2
DYNLT2B	ENST00000446494.1 linkuse as main transcript	c.*37-67G>A	intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0654

AC:

9956

AN:

152134

Hom.:

379

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0760

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.0447

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.0169

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.0372

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0648

Gnomad OTH

AF:

0.0611

GnomAD4 exome

AF:

0.0653

AC:

76540

AN:

1171278

Hom.:

2989

Cov.:

AF XY:

0.0682

AC XY:

40655

AN XY:

596286

show subpopulations

Gnomad4 AFR exome

AF:

0.0746

Gnomad4 AMR exome

AF:

0.0336

Gnomad4 ASJ exome

AF:

0.112

Gnomad4 EAS exome

AF:

0.0170

Gnomad4 SAS exome

AF:

0.121

Gnomad4 FIN exome

AF:

0.0404

Gnomad4 NFE exome

AF:

0.0630

Gnomad4 OTH exome

AF:

0.0732

GnomAD4 genome

AF:

0.0654

AC:

9960

AN:

152252

Hom.:

380

Cov.:

AF XY:

0.0659

AC XY:

4902

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.0760

Gnomad4 AMR

AF:

0.0446

Gnomad4 ASJ

AF:

0.112

Gnomad4 EAS

AF:

0.0167

Gnomad4 SAS

AF:

0.123

Gnomad4 FIN

AF:

0.0372

Gnomad4 NFE

AF:

0.0648

Gnomad4 OTH

AF:

0.0605

Alfa

AF:

0.0678

Hom.:

Bravo

AF:

0.0652

Asia WGS

AF:

0.0620

AC:

217

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.024

DANN

Benign

0.57

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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