rs11079337

chr17-58085135-C-Achr17-58085135-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080677.3(DYNLL2):c.-10+1452C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 152,010 control chromosomes in the GnomAD database, including 28,674 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 0.59 (28674 hom., cov: 32)
• Consequence: DYNLL2 NM_080677.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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/exons	MANE	UniProt
DYNLL2	NM_080677.3	c.-10+1452C>A		intron_variant		ENST00000579991.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DYNLL2	ENST00000579991.3	c.-10+1452C>A		intron_variant		1	NM_080677.3	P1

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89424 AN: 151892 Hom.: 28664 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.588 AC: 89455 AN: 152010 Hom.: 28674 Cov.: 32 AF XY: 0.599 AC XY: 44517 AN XY: 74286

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.786

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.635

Alfa AF: 0.634 Hom.: 31665

Bravo AF: 0.574

Asia WGS AF: 0.815 AC: 2835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.66
Dann	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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

Other links and lift over

dbSNP: rs11079337; hg19: chr17-56162496;