rs4964879
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003565.4(ULK1):c.1610-127G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,326,766 control chromosomes in the GnomAD database, including 22,896 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 0.22 ( 5083 hom., cov: 33)
Exomes 𝑓: 0.14 ( 17813 hom. )
Consequence
ULK1
NM_003565.4 intron
NM_003565.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.147
Genes affected
ULK1 (HGNC:12558): (unc-51 like autophagy activating kinase 1) Enables identical protein binding activity; protein serine/threonine kinase activity; and small GTPase binding activity. Involved in several processes, including autophagosome assembly; positive regulation by symbiont of host autophagy; and protein phosphorylation. Located in autophagosome; cytosol; and phagophore assembly site membrane. Is extrinsic component of autophagosome membrane; extrinsic component of omegasome membrane; and extrinsic component of phagophore assembly site membrane. Part of Atg1/ULK1 kinase complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ULK1 | NM_003565.4 | c.1610-127G>A | intron_variant | ENST00000321867.6 | |||
ULK1 | XM_011538798.4 | c.1679-127G>A | intron_variant | ||||
ULK1 | XM_011538799.3 | c.1592-127G>A | intron_variant | ||||
ULK1 | XR_007063134.1 | n.2059-127G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ULK1 | ENST00000321867.6 | c.1610-127G>A | intron_variant | 1 | NM_003565.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.218 AC: 33147AN: 151946Hom.: 5085 Cov.: 33
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GnomAD4 exome AF: 0.143 AC: 168288AN: 1174702Hom.: 17813 AF XY: 0.141 AC XY: 83142AN XY: 589346
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GnomAD4 genome ? AF: 0.218 AC: 33162AN: 152064Hom.: 5083 Cov.: 33 AF XY: 0.219 AC XY: 16279AN XY: 74324
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at