rs138423863
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PM4_SupportingBP6_Very_StrongBA1
The NM_014915.3(ANKRD26):βc.1596_1598delβ(p.Glu533del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0172 in 1,611,050 control chromosomes in the GnomAD database, including 1,828 homozygotes. Variant has been reported in ClinVar as Likely benign (β β ).
Frequency
Genomes: π 0.018 ( 150 hom., cov: 32)
Exomes π: 0.017 ( 1678 hom. )
Consequence
ANKRD26
NM_014915.3 inframe_deletion
NM_014915.3 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.70
Genes affected
ANKRD26 (HGNC:29186): (ankyrin repeat domain containing 26) This gene encodes a protein containing N-terminal ankyrin repeats which function in protein-protein interactions. Mutations in this gene are associated with autosomal dominant thrombocytopenia-2. Pseudogenes of this gene are found on chromosome 7, 10, 13 and 16. 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 -15 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_014915.3. Strenght limited to Supporting due to length of the change: 1aa.
BP6
?
Variant 10-27053356-CTCT-C is Benign according to our data. Variant chr10-27053356-CTCT-C is described in ClinVar as [Likely_benign]. Clinvar id is 260460.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-27053356-CTCT-C is described in Lovd as [Likely_benign].
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKRD26 | NM_014915.3 | c.1596_1598del | p.Glu533del | inframe_deletion | 16/34 | ENST00000376087.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKRD26 | ENST00000376087.5 | c.1596_1598del | p.Glu533del | inframe_deletion | 16/34 | 5 | NM_014915.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0181 AC: 2748AN: 152014Hom.: 152 Cov.: 32
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GnomAD3 exomes AF: 0.0362 AC: 8988AN: 248570Hom.: 481 AF XY: 0.0393 AC XY: 5300AN XY: 134958
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GnomAD4 exome AF: 0.0171 AC: 24910AN: 1458918Hom.: 1678 AF XY: 0.0198 AC XY: 14393AN XY: 725792
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GnomAD4 genome ? AF: 0.0181 AC: 2749AN: 152132Hom.: 150 Cov.: 32 AF XY: 0.0235 AC XY: 1750AN XY: 74360
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 26, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 02, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Thrombocytopenia 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Thrombocytopenia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at