chr17-19779014-G-A

Variant names:

• chr17-19779014-G-A
• rs205096
• NM_014683.4:c.2917-1298C>T

Variant summary

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

The NM_014683.4(ULK2):​c.2917-1298C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.944 in 152,280 control chromosomes in the GnomAD database, including 68,081 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 0.94 (68081 hom., cov: 32)
• Consequence: ULK2 NM_014683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480
• Publications: 2 publications found

Genes affected

ULK2 (HGNC:13480): (unc-51 like autophagy activating kinase 2) This gene encodes a protein that is similar to a serine/threonine kinase in C. elegans which is involved in axonal elongation. The structure of this protein is similar to the C. elegans protein in that both proteins have an N-terminal kinase domain, a central proline/serine rich (PS) domain, and a C-terminal (C) domain. The gene is located within the Smith-Magenis syndrome region on chromosome 17. Alternatively spliced transcript variants encoding the same protein have been identified. [provided by RefSeq, Dec 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ULK2	NM_014683.4	c.2917-1298C>T		intron_variant	Intron 25 of 26	ENST00000395544.9	NP_055498.3
ULK2	NM_001142610.2	c.2917-1298C>T		intron_variant	Intron 25 of 27		NP_001136082.1
ULK2	XM_017025425.3	c.2980-1298C>T		intron_variant	Intron 25 of 27		XP_016880914.1
ULK2	XM_047437147.1	c.2836-1298C>T		intron_variant	Intron 25 of 27		XP_047293103.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ULK2	ENST00000395544.9	c.2917-1298C>T		intron_variant	Intron 25 of 26	1	NM_014683.4	ENSP00000378914.4
ULK2	ENST00000361658.6	c.2917-1298C>T		intron_variant	Intron 25 of 27	1		ENSP00000354877.2

Frequencies

GnomAD3 genomes AF: 0.944 AC: 143707 AN: 152162 Hom.: 68031 Cov.: 32

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.968

Gnomad OTH AF: 0.950

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.944 AC: 143816 AN: 152280 Hom.: 68081 Cov.: 32 AF XY: 0.942 AC XY: 70125 AN XY: 74454

African (AFR) AF: 0.934 AC: 38819 AN: 41544

American (AMR) AF: 0.929 AC: 14209 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.983 AC: 3413 AN: 3472

East Asian (EAS) AF: 0.761 AC: 3937 AN: 5176

South Asian (SAS) AF: 0.845 AC: 4078 AN: 4826

European-Finnish (FIN) AF: 0.970 AC: 10296 AN: 10610

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.968 AC: 65867 AN: 68044

Other (OTH) AF: 0.950 AC: 2006 AN: 2112

Alfa AF: 0.953 Hom.: 11975

Bravo AF: 0.943

Asia WGS AF: 0.794 AC: 2761 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.32
PhyloP100		0.048
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: rs205096; hg19: chr17-19682327;