Genetic Variant DYNLL2:c.*1731G>A (chr17-58091010-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_080677.3(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
NM_080677.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.216

Publications

10 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080677.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNLL2	NM_080677.3	MANE Select	c.*1731G>A		3_prime_UTR	Exon 3 of 3	NP_542408.1	Q96FJ2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DYNLL2	ENST00000579991.3	TSL:1 MANE Select	c.*1731G>A	3_prime_UTR	Exon 3 of 3	ENSP00000477310.1	Q96FJ2
DYNLL2	ENST00000908491.1		c.*1731G>A	3_prime_UTR	Exon 2 of 2	ENSP00000578550.1
DYNLL2	ENST00000908492.1		c.*1731G>A	3_prime_UTR	Exon 3 of 3	ENSP00000578551.1

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

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.700

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.815

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.439

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.798

AC:

121285

AN:

151906

Hom.:

48552

Cov.:

AF XY:

0.803

AC XY:

59637

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.817

AC:

33822

AN:

41374

American (AMR)

AF:

0.822

AC:

12554

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.824

AC:

2859

AN:

3470

East Asian (EAS)

AF:

0.911

AC:

4711

AN:

5174

South Asian (SAS)

AF:

0.833

AC:

4003

AN:

4806

European-Finnish (FIN)

AF:

0.808

AC:

8539

AN:

10562

Middle Eastern (MID)

AF:

0.801

AC:

234

AN:

292

European-Non Finnish (NFE)

AF:

0.767

AC:

52136

AN:

67942

Other (OTH)

AF:

0.793

AC:

1663

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1189

2379

3568

4758

5947

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

870

1740

2610

3480

4350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.776

Hom.:

34188

Bravo

AF:

0.798

Asia WGS

AF:

0.872

AC:

3031

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

1.2

(source)

DANN

Benign

0.67

PhyloP100

0.22

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over