17-58092402-A-G

Position:

• chr17-58092402-A-G

Variant summary

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

The NM_080677.3(DYNLL2):​c.*3123A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 152,262 control chromosomes in the GnomAD database, including 48,823 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 (48808 hom., cov: 32)
  • Exomes 𝑓: 0.78 (15 hom.)
• Consequence: DYNLL2 NM_080677.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540

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=-0.84).
• 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	c.*3123A>G		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	c.*3123A>G		3_prime_UTR_variant	3/3	1	NM_080677.3	ENSP00000477310.1

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121631 AN: 152094 Hom.: 48760 Cov.: 32

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.795

GnomAD4 exome AF: 0.780 AC: 39 AN: 50 Hom.: 15 Cov.: 0 AF XY: 0.765 AC XY: 26 AN XY: 34

Gnomad4 AFR exome AF: 0.750

Gnomad4 AMR exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.775

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.800 AC: 121734 AN: 152212 Hom.: 48808 Cov.: 32 AF XY: 0.805 AC XY: 59870 AN XY: 74404

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.849

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.834

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.796

Alfa AF: 0.773 Hom.: 71409

Bravo AF: 0.799

Asia WGS AF: 0.873 AC: 3037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.2
DANN	Benign	0.88

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: rs9900038; hg19: chr17-56169763;