Variant rs10132 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000579991.3(DYNLL2):c.*1731G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 151,986 control chromosomes in the GnomAD database, including 48,577 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 0.80 ( 48552 hom., cov: 29)

Exomes 𝑓: 0.80 ( 25 hom. )

Consequence

DYNLL2
ENST00000579991.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.216

Variant links:

Genes affected

DYNLL2 (HGNC:24596): (dynein light chain LC8-type 2) Predicted to enable dynein intermediate chain binding activity and dynein light intermediate chain binding activity. Predicted to be involved in cilium assembly. Located in 9+0 non-motile cilium and centrosome. Is active in glutamatergic synapse and postsynapse. [provided by Alliance of Genome Resources, Apr 2022]

DYNLL2 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=-0.76).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DYNLL2	NM_080677.3 linkuse as main transcript	c.*1731G>A		3_prime_UTR_variant	3/3	ENST00000579991.3	NP_542408.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DYNLL2	ENST00000579991.3 linkuse as main transcript	c.*1731G>A		3_prime_UTR_variant	3/3	1	NM_080677.3	ENSP00000477310	P1

Frequencies

GnomAD3 genomes

AF:

0.798

AC:

121182

AN:

151788

Hom.:

48504

Cov.:

show subpopulations

Gnomad AFR

AF:

0.817

Gnomad AMI

AF:

0.838

Gnomad AMR

AF:

0.822

Gnomad ASJ

AF:

0.824

Gnomad EAS

AF:

0.911

Gnomad SAS

AF:

0.834

Gnomad FIN

AF:

0.808

Gnomad MID

AF:

0.812

Gnomad NFE

AF:

0.767

Gnomad OTH

AF:

0.791

GnomAD4 exome

AF:

0.800

AC:

AN:

Hom.:

Cov.:

AF XY:

0.768

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.700

Gnomad4 NFE exome

AF:

0.815

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.798

AC:

121285

AN:

151906

Hom.:

48552

Cov.:

AF XY:

0.803

AC XY:

59637

AN XY:

74254

show subpopulations

Gnomad4 AFR

AF:

0.817

Gnomad4 AMR

AF:

0.822

Gnomad4 ASJ

AF:

0.824

Gnomad4 EAS

AF:

0.911

Gnomad4 SAS

AF:

0.833

Gnomad4 FIN

AF:

0.808

Gnomad4 NFE

AF:

0.767

Gnomad4 OTH

AF:

0.793

Alfa

AF:

0.776

Hom.:

28093

Bravo

AF:

0.798

Asia WGS

AF:

0.872

AC:

3031

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

1.2

DANN

Benign

0.67

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