11-68061977-A-G
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001277.3(CHKA):āc.1290T>Cā(p.Ile430=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000188 in 1,597,644 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 (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 32)
Exomes š: 0.0000014 ( 0 hom. )
Consequence
CHKA
NM_001277.3 synonymous
NM_001277.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.205
Genes affected
CHKA (HGNC:1937): (choline kinase alpha) The major pathway for the biosynthesis of phosphatidylcholine occurs via the CDP-choline pathway. The protein encoded by this gene is the initial enzyme in the sequence and may play a regulatory role. The encoded protein also catalyzes the phosphorylation of ethanolamine. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
Variant 11-68061977-A-G is Benign according to our data. Variant chr11-68061977-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2642028.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.205 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHKA | NM_001277.3 | c.1290T>C | p.Ile430= | synonymous_variant | 11/12 | ENST00000265689.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHKA | ENST00000265689.9 | c.1290T>C | p.Ile430= | synonymous_variant | 11/12 | 1 | NM_001277.3 | ||
CHKA | ENST00000356135.9 | c.1236T>C | p.Ile412= | synonymous_variant | 10/11 | 1 | P1 | ||
CHKA | ENST00000525155.5 | c.306T>C | p.Ile102= | synonymous_variant, NMD_transcript_variant | 4/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000138 AC: 2AN: 1445408Hom.: 0 Cov.: 30 AF XY: 0.00000139 AC XY: 1AN XY: 716942
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74378
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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 | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | CHKA: BP4, BP7 - |
Computational scores
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Benign
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Benign
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Benign
RBP_binding_hub_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at