17-58093234-C-T

Position:

• chr17-58093234-C-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190

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=-0.91).
• 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/exons	MANE	UniProt
DYNLL2	NM_080677.3	c.*3955C>T		3_prime_UTR_variant	3/3	ENST00000579991.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DYNLL2	ENST00000579991.3	c.*3955C>T		3_prime_UTR_variant	3/3	1	NM_080677.3	P1

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92689 AN: 151940 Hom.: 30918 Cov.: 32

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: 6 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 6 AN XY: 12

Gnomad4 ASJ exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.610 AC: 92717 AN: 152058 Hom.: 30925 Cov.: 32 AF XY: 0.621 AC XY: 46134 AN XY: 74336

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

Other links and lift over

dbSNP: rs9902118; hg19: chr17-56170595;