rs1625226
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_017886.4(ULK4):c.1288-9A>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.946 in 1,348,298 control chromosomes in the GnomAD database, including 604,270 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.93 ( 65894 hom., cov: 30)
Exomes 𝑓: 0.95 ( 538376 hom. )
Consequence
ULK4
NM_017886.4 splice_polypyrimidine_tract, intron
NM_017886.4 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00002206
2
Clinical Significance
Conservation
PhyloP100: -0.694
Genes affected
ULK4 (HGNC:15784): (unc-51 like kinase 4) This gene encodes a member of the unc-51-like serine/threonine kinase (STK) family. Members of this protein family play a role in neuronal growth and endocytosis. The encoded protein is likely involved in neurite branching, neurite elongation and neuronal migration. Genome-wide association studies (GWAS) indicate an association of variations in this gene with blood pressure and hypertension. Sequence variations in this gene may also be be associated with psychiatric disorders, including schizophrenia and bipolar disorder. Pseudogenes associated with this gene have been identified and are located on chromosome 15. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
Variant 3-41898501-T-A is Benign according to our data. Variant chr3-41898501-T-A is described in ClinVar as [Benign]. Clinvar id is 403588.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ULK4 | NM_017886.4 | c.1288-9A>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000301831.9 | |||
ULK4 | NM_001322500.2 | c.1288-9A>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
ULK4 | NM_001322501.2 | c.382-9A>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
ULK4 | NR_136342.2 | n.1354-9A>T | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ULK4 | ENST00000301831.9 | c.1288-9A>T | splice_polypyrimidine_tract_variant, intron_variant | 2 | NM_017886.4 | P1 | |||
ULK4 | ENST00000420927.5 | c.1288-9A>T | splice_polypyrimidine_tract_variant, intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.928 AC: 140227AN: 151144Hom.: 65867 Cov.: 30
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GnomAD3 exomes AF: 0.934 AC: 192017AN: 205578Hom.: 89653 AF XY: 0.939 AC XY: 104538AN XY: 111376
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GnomAD4 exome AF: 0.949 AC: 1135678AN: 1197038Hom.: 538376 Cov.: 22 AF XY: 0.949 AC XY: 565285AN XY: 595600
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GnomAD4 genome ? AF: 0.928 AC: 140299AN: 151260Hom.: 65894 Cov.: 30 AF XY: 0.929 AC XY: 68711AN XY: 73930
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
Source:
Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at