17-58092402-A-G

Variant names:

• chr17-58092402-A-G
• rs9900038
• NM_080677.3:c.*3123A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DYNLL2	NM_080677.3	c.*3123A>G		3_prime_UTR_variant	Exon 3 of 3	ENST00000579991.3	NP_542408.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DYNLL2	ENST00000579991.3	c.*3123A>G		3_prime_UTR_variant	Exon 3 of 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

African (AFR) AF: 0.750 AC: 3 AN: 4

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.775 AC: 31 AN: 40

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.818 AC: 33976 AN: 41522

American (AMR) AF: 0.822 AC: 12576 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2946 AN: 3472

East Asian (EAS) AF: 0.911 AC: 4710 AN: 5170

South Asian (SAS) AF: 0.834 AC: 4024 AN: 4824

European-Finnish (FIN) AF: 0.809 AC: 8585 AN: 10608

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52235 AN: 67998

Other (OTH) AF: 0.796 AC: 1681 AN: 2112

Alfa AF: 0.779 Hom.: 131665

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
PhyloP100		0.054
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9900038; hg19: chr17-56169763;