rs7300908
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003565.4(ULK1):c.2962-224C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000249 in 602,898 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000011 ( 0 hom. )
Consequence
ULK1
NM_003565.4 intron
NM_003565.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.79
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 Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ULK1 | NM_003565.4 | c.2962-224C>G | intron_variant | ENST00000321867.6 | |||
ULK1 | XM_011538798.4 | c.3031-224C>G | intron_variant | ||||
ULK1 | XM_011538799.3 | c.2944-224C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ULK1 | ENST00000321867.6 | c.2962-224C>G | intron_variant | 1 | NM_003565.4 | P1 | |||
ULK1 | ENST00000540568.1 | n.810C>G | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
ULK1 | ENST00000540647.5 | n.831-224C>G | intron_variant, non_coding_transcript_variant | 2 | |||||
ULK1 | ENST00000544718.1 | n.897-224C>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152150Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.0000111 AC: 5AN: 450748Hom.: 0 Cov.: 6 AF XY: 0.0000129 AC XY: 3AN XY: 232660
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GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152150Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74330
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at