15-74836160-T-C

Position:

• chr15-74836160-T-C

Variant summary

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

The NM_001099436.4(ULK3):​c.*1068A>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 0.682 in 152,118 control chromosomes in the GnomAD database, including 35,560 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 0.68 (35559 hom., cov: 33)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: ULK3 NM_001099436.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.958

Genes affected

ULK3 (HGNC:19703): (unc-51 like kinase 3) Enables protein serine/threonine kinase activity. Involved in several processes, including fibroblast activation; protein autophosphorylation; and regulation of smoothened signaling pathway. Located in cytoplasm. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ULK3	NM_001099436.4	c.*1068A>G		3_prime_UTR_variant	16/16	ENST00000440863.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ULK3	ENST00000440863.7	c.*1068A>G		3_prime_UTR_variant	16/16	2	NM_001099436.4	A1

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103722 AN: 151994 Hom.: 35533 Cov.: 33

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.671

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.682 AC: 103803 AN: 152112 Hom.: 35559 Cov.: 33 AF XY: 0.680 AC XY: 50533 AN XY: 74348

Gnomad4 AFR AF: 0.627

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.673

Alfa AF: 0.701 Hom.: 47469

Bravo AF: 0.683

Asia WGS AF: 0.730 AC: 2538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.36
DANN	Benign	0.34
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs9210; hg19: chr15-75128501;