Variant chr3-196317798-C-G 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.113+242G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,062 control chromosomes in the GnomAD database, including 9,063 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.32 ( 9063 hom., cov: 31)

Consequence

DYNLT2B
NM_152773.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.14

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:

TM4SF19-DYNLT2B (HGNC:):

TM4SF19-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=-0.82).

BP6

Variant 3-196317798-C-G is Benign according to our data. Variant chr3-196317798-C-G is described in ClinVar as [Benign]. Clinvar id is 1288668.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
DYNLT2B	NM_152773.5 linkuse as main transcript	c.113+242G>C	intron_variant	ENST00000325318.10
TM4SF19-DYNLT2B	NR_037950.1 linkuse as main transcript	n.862-1567G>C	intron_variant, non_coding_transcript_variant
DYNLT2B	NM_001351628.2 linkuse as main transcript	c.113+242G>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
DYNLT2B	ENST00000325318.10 linkuse as main transcript	c.113+242G>C	intron_variant	1	NM_152773.5	P1
DYNLT2B	ENST00000426563.5 linkuse as main transcript	c.117+238G>C	intron_variant, NMD_transcript_variant	2
DYNLT2B	ENST00000446494.1 linkuse as main transcript	c.113+242G>C	intron_variant, NMD_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.325

AC:

49322

AN:

151944

Hom.:

9055

Cov.:

show subpopulations

Gnomad AFR

AF:

0.237

Gnomad AMI

AF:

0.195

Gnomad AMR

AF:

0.419

Gnomad ASJ

AF:

0.364

Gnomad EAS

AF:

0.834

Gnomad SAS

AF:

0.463

Gnomad FIN

AF:

0.264

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.318

Gnomad OTH

AF:

0.338

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.325

AC:

49357

AN:

152062

Hom.:

9063

Cov.:

AF XY:

0.331

AC XY:

24621

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.237

Gnomad4 AMR

AF:

0.419

Gnomad4 ASJ

AF:

0.364

Gnomad4 EAS

AF:

0.834

Gnomad4 SAS

AF:

0.462

Gnomad4 FIN

AF:

0.264

Gnomad4 NFE

AF:

0.318

Gnomad4 OTH

AF:

0.343

Alfa

AF:

0.310

Hom.:

959

Bravo

AF:

0.334

Asia WGS

AF:

0.595

AC:

2064

AN:

3468

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 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.89

DANN

Benign

0.50

RBP_binding_hub_radar

0.67

RBP_regulation_power_radar

1.8

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.10

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