chr17-19781102-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_014683.4(ULK2):c.2642G>A(p.Arg881Gln) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00167 in 1,613,556 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0069 ( 16 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 19 hom. )
Consequence
ULK2
NM_014683.4 missense, splice_region
NM_014683.4 missense, splice_region
Scores
1
16
Clinical Significance
Conservation
PhyloP100: 3.85
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 17-19781102-C-T is Benign according to our data. Variant chr17-19781102-C-T is described in ClinVar as [Benign]. Clinvar id is 718298.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00693 (1056/152272) while in subpopulation AFR AF= 0.0229 (951/41546). AF 95% confidence interval is 0.0217. There are 16 homozygotes in gnomad4. There are 519 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 16 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ULK2 | NM_014683.4 | c.2642G>A | p.Arg881Gln | missense_variant, splice_region_variant | 24/27 | ENST00000395544.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ULK2 | ENST00000395544.9 | c.2642G>A | p.Arg881Gln | missense_variant, splice_region_variant | 24/27 | 1 | NM_014683.4 | P1 | |
ULK2 | ENST00000361658.6 | c.2642G>A | p.Arg881Gln | missense_variant, splice_region_variant | 24/28 | 1 | P1 | ||
ULK2 | ENST00000571454.2 | n.546G>A | splice_region_variant, non_coding_transcript_exon_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00693 AC: 1054AN: 152154Hom.: 16 Cov.: 32
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GnomAD3 exomes AF: 0.00197 AC: 491AN: 249050Hom.: 7 AF XY: 0.00154 AC XY: 208AN XY: 134706
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GnomAD4 exome AF: 0.00112 AC: 1641AN: 1461284Hom.: 19 Cov.: 31 AF XY: 0.00101 AC XY: 733AN XY: 726910
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GnomAD4 genome ? AF: 0.00693 AC: 1056AN: 152272Hom.: 16 Cov.: 32 AF XY: 0.00697 AC XY: 519AN XY: 74462
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MVP
MPC
0.16
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at