rs146159734
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_014915.3(ANKRD26):c.4259G>A(p.Cys1420Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00229 in 1,613,164 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C1420F) has been classified as Uncertain significance.
Frequency
Consequence
NM_014915.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKRD26 | NM_014915.3 | c.4259G>A | p.Cys1420Tyr | missense_variant | 30/34 | ENST00000376087.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKRD26 | ENST00000376087.5 | c.4259G>A | p.Cys1420Tyr | missense_variant | 30/34 | 5 | NM_014915.3 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00170 AC: 259AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00333 AC: 826AN: 248244Hom.: 11 AF XY: 0.00383 AC XY: 516AN XY: 134676
GnomAD4 exome AF: 0.00235 AC: 3438AN: 1460872Hom.: 26 Cov.: 31 AF XY: 0.00266 AC XY: 1930AN XY: 726742
GnomAD4 genome AF: 0.00169 AC: 258AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.00180 AC XY: 134AN XY: 74468
ClinVar
Submissions by phenotype
Thrombocytopenia 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 01, 2021 | This variant is associated with the following publications: (PMID: 29185836, 27931139, 28748566) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 15, 2016 | - - |
ANKRD26-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 05, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at