Genetic Variant DYNLL2:c.*3955C>T (chr17-58093234-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_080677.3(DYNLL2):c.*3955C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 152,070 control chromosomes in the GnomAD database, including 30,925 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 0.61 ( 30925 hom., cov: 32)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

DYNLL2
NM_080677.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.190

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DYNLL2	NM_080677.3 link	c.*3955C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000579991.3	NP_542408.1	Q96FJ2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DYNLL2	ENST00000579991.3 link	c.*3955C>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_080677.3	ENSP00000477310.1		Q96FJ2

Frequencies

GnomAD3 genomes

AF:

0.610

AC:

92689

AN:

151940

Hom.:

30918

Cov.:

show subpopulations

Gnomad AFR

AF:

0.329

Gnomad AMI

AF:

0.737

Gnomad AMR

AF:

0.724

Gnomad ASJ

AF:

0.744

Gnomad EAS

AF:

0.910

Gnomad SAS

AF:

0.822

Gnomad FIN

AF:

0.728

Gnomad MID

AF:

0.656

Gnomad NFE

AF:

0.689

Gnomad OTH

AF:

0.647

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.500

GnomAD4 genome

AF:

0.610

AC:

92717

AN:

152058

Hom.:

30925

Cov.:

AF XY:

0.621

AC XY:

46134

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.329

Gnomad4 AMR

AF:

0.724

Gnomad4 ASJ

AF:

0.744

Gnomad4 EAS

AF:

0.910

Gnomad4 SAS

AF:

0.821

Gnomad4 FIN

AF:

0.728

Gnomad4 NFE

AF:

0.689

Gnomad4 OTH

AF:

0.649

Alfa

AF:

0.646

Hom.:

4162

Bravo

AF:

0.592

Asia WGS

AF:

0.827

AC:

2877

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

5.3

DANN

Benign

0.56

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