4-112382381-A-G
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_025144.4(ALPK1):c.122-17A>G 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 0.00000559 in 1,608,934 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000067 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000055 ( 0 hom. )
Consequence
ALPK1
NM_025144.4 splice_polypyrimidine_tract, intron
NM_025144.4 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.571
Genes affected
ALPK1 (HGNC:20917): (alpha kinase 1) This gene encodes an alpha kinase. Mice which were homozygous for disrupted copies of this gene exhibited coordination defects (PMID: 21208416). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BP6
Variant 4-112382381-A-G is Benign according to our data. Variant chr4-112382381-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2995833.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 8 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALPK1 | NM_025144.4 | c.122-17A>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000650871.1 | NP_079420.3 | |||
ALPK1 | NM_001102406.2 | c.122-17A>G | splice_polypyrimidine_tract_variant, intron_variant | NP_001095876.1 | ||||
ALPK1 | NM_001253884.2 | c.42+4483A>G | intron_variant | NP_001240813.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALPK1 | ENST00000650871.1 | c.122-17A>G | splice_polypyrimidine_tract_variant, intron_variant | NM_025144.4 | ENSP00000498374 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000673 AC: 1AN: 148662Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251136Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135754
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GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460272Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726392
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GnomAD4 genome AF: 0.00000673 AC: 1AN: 148662Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 1AN XY: 72308
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 10, 2023 | - - |
Computational 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