Variant chr2-43774077-C-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_016008.4(DYNC2LI1):c.-62C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0235 in 1,607,612 control chromosomes in the GnomAD database, including 823 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.045 ( 303 hom., cov: 32)

Exomes 𝑓: 0.021 ( 520 hom. )

Consequence

DYNC2LI1
NM_016008.4 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.808

Variant links:

Genes affected

DYNC2LI1 (HGNC:24595): (dynein cytoplasmic 2 light intermediate chain 1) This gene encodes a protein that is a component of the dynein-2 microtubule motor protein complex that plays a role in the retrograde transport of cargo in primary cilia via the intraflagellar transport system. This gene is ubiquitously expressed and its protein, which localizes to the axoneme and Golgi apparatus, interacts directly with the cytoplasmic dynein 2 heavy chain 1 protein to form part of the multi-protein dynein-2 complex. Mutations in this gene produce defects in the dynein-2 complex which result in several types of ciliopathy including short-rib thoracic dysplasia 15 with polydactyly (SRTD15). Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Feb 2017]

DYNC2LI1 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=-0.85).

BP6

Variant 2-43774077-C-T is Benign according to our data. Variant chr2-43774077-C-T is described in ClinVar as [Benign]. Clinvar id is 1246768.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DYNC2LI1	NM_016008.4 linkuse as main transcript	c.-62C>T		5_prime_UTR_variant	1/13	ENST00000260605.12	NP_057092.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DYNC2LI1	ENST00000260605.12 linkuse as main transcript	c.-62C>T		5_prime_UTR_variant	1/13	1	NM_016008.4	ENSP00000260605	P4	Q8TCX1-1

Frequencies

GnomAD3 genomes

AF:

0.0451

AC:

6859

AN:

152202

Hom.:

301

Cov.:

show subpopulations

Gnomad AFR

AF:

0.111

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0232

Gnomad ASJ

AF:

0.0277

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.0203

Gnomad FIN

AF:

0.0194

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0208

Gnomad OTH

AF:

0.0407

GnomAD4 exome

AF:

0.0212

AC:

30856

AN:

1455292

Hom.:

520

Cov.:

AF XY:

0.0213

AC XY:

15385

AN XY:

723608

show subpopulations

Gnomad4 AFR exome

AF:

0.119

Gnomad4 AMR exome

AF:

0.0211

Gnomad4 ASJ exome

AF:

0.0264

Gnomad4 EAS exome

AF:

0.0000254

Gnomad4 SAS exome

AF:

0.0185

Gnomad4 FIN exome

AF:

0.0179

Gnomad4 NFE exome

AF:

0.0191

Gnomad4 OTH exome

AF:

0.0237

GnomAD4 genome

AF:

0.0451

AC:

6867

AN:

152320

Hom.:

303

Cov.:

AF XY:

0.0444

AC XY:

3303

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.111

Gnomad4 AMR

AF:

0.0231

Gnomad4 ASJ

AF:

0.0277

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0203

Gnomad4 FIN

AF:

0.0194

Gnomad4 NFE

AF:

0.0208

Gnomad4 OTH

AF:

0.0402

Alfa

AF:

0.0331

Hom.:

Bravo

AF:

0.0480

Asia WGS

AF:

0.0170

AC:

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 12, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

6.4

DANN

Benign

0.82

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.0

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over