chr17-58091010-G-A

Variant names:

• chr17-58091010-G-A
• rs10132
• NM_080677.3:c.*1731G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080677.3(DYNLL2):​c.*1731G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 151,986 control chromosomes in the GnomAD database, including 48,577 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 (48552 hom., cov: 29)
  • Exomes 𝑓: 0.80 (25 hom.)
• Consequence: DYNLL2 NM_080677.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216
• Publications: 10 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=-0.76).
• 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.*1731G>A		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.*1731G>A		3_prime_UTR_variant	Exon 3 of 3	1	NM_080677.3	ENSP00000477310.1

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121182 AN: 151788 Hom.: 48504 Cov.: 29

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.791

GnomAD4 exome AF: 0.800 AC: 64 AN: 80 Hom.: 25 Cov.: 0 AF XY: 0.768 AC XY: 43 AN XY: 56

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.700 AC: 14 AN: 20

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.815 AC: 44 AN: 54

Other (OTH) AF: 1.00 AC: 6 AN: 6

GnomAD4 genome AF: 0.798 AC: 121285 AN: 151906 Hom.: 48552 Cov.: 29 AF XY: 0.803 AC XY: 59637 AN XY: 74254

African (AFR) AF: 0.817 AC: 33822 AN: 41374

American (AMR) AF: 0.822 AC: 12554 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2859 AN: 3470

East Asian (EAS) AF: 0.911 AC: 4711 AN: 5174

South Asian (SAS) AF: 0.833 AC: 4003 AN: 4806

European-Finnish (FIN) AF: 0.808 AC: 8539 AN: 10562

Middle Eastern (MID) AF: 0.801 AC: 234 AN: 292

European-Non Finnish (NFE) AF: 0.767 AC: 52136 AN: 67942

Other (OTH) AF: 0.793 AC: 1663 AN: 2098

Alfa AF: 0.776 Hom.: 34188

Bravo AF: 0.798

Asia WGS AF: 0.872 AC: 3031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		0.22
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs10132; hg19: chr17-56168371;