rs1717003
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1
The NM_017886.4(ULK4):c.1577+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,060 control chromosomes in the GnomAD database, including 39,433 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.69 ( 39433 hom., cov: 32)
Exomes 𝑓: 0.81 ( 422173 hom. )
Failed GnomAD Quality Control
Consequence
ULK4
NM_017886.4 intron
NM_017886.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0970
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
?
Variant 3-41895508-C-T is Benign according to our data. Variant chr3-41895508-C-T is described in ClinVar as [Benign]. Clinvar id is 403586.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ULK4 | NM_017886.4 | c.1577+10G>A | intron_variant | ENST00000301831.9 | |||
ULK4 | NM_001322500.2 | c.1577+10G>A | intron_variant | ||||
ULK4 | NM_001322501.2 | c.671+10G>A | intron_variant | ||||
ULK4 | NR_136342.2 | n.1643+10G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ULK4 | ENST00000301831.9 | c.1577+10G>A | intron_variant | 2 | NM_017886.4 | P1 | |||
ULK4 | ENST00000420927.5 | c.1577+10G>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.689 AC: 104670AN: 151940Hom.: 39415 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
104670
AN:
151940
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.769 AC: 101864AN: 132404Hom.: 40349 AF XY: 0.776 AC XY: 56396AN XY: 72702
GnomAD3 exomes
AF:
AC:
101864
AN:
132404
Hom.:
AF XY:
AC XY:
56396
AN XY:
72702
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.815 AC: 1025270AN: 1258108Hom.: 422173 Cov.: 18 AF XY: 0.816 AC XY: 510323AN XY: 625068
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1025270
AN:
1258108
Hom.:
Cov.:
18
AF XY:
AC XY:
510323
AN XY:
625068
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.689 AC: 104705AN: 152060Hom.: 39433 Cov.: 32 AF XY: 0.690 AC XY: 51280AN XY: 74336
GnomAD4 genome
?
AF:
AC:
104705
AN:
152060
Hom.:
Cov.:
32
AF XY:
AC XY:
51280
AN XY:
74336
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2784
AN:
3460
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
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at