rs12572862
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_014915.3(ANKRD26):āc.3658G>Cā(p.Val1220Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0168 in 1,608,624 control chromosomes in the GnomAD database, including 1,801 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
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.3658G>C | p.Val1220Leu | missense_variant | 25/34 | ENST00000376087.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKRD26 | ENST00000376087.5 | c.3658G>C | p.Val1220Leu | missense_variant | 25/34 | 5 | NM_014915.3 | A2 | |
ANKRD26 | ENST00000436985.7 | c.3655G>C | p.Val1219Leu | missense_variant | 25/34 | 1 | P4 | ||
ANKRD26 | ENST00000675936.1 | c.76G>C | p.Val26Leu | missense_variant, NMD_transcript_variant | 2/13 | ||||
ANKRD26 | ENST00000675116.1 | c.1309G>C | p.Val437Leu | missense_variant, NMD_transcript_variant | 5/15 |
Frequencies
GnomAD3 genomes ? AF: 0.0165 AC: 2509AN: 152080Hom.: 158 Cov.: 32
GnomAD3 exomes AF: 0.0357 AC: 8895AN: 249158Hom.: 465 AF XY: 0.0388 AC XY: 5250AN XY: 135166
GnomAD4 exome AF: 0.0169 AC: 24559AN: 1456426Hom.: 1645 Cov.: 31 AF XY: 0.0196 AC XY: 14192AN XY: 724464
GnomAD4 genome ? AF: 0.0165 AC: 2505AN: 152198Hom.: 156 Cov.: 32 AF XY: 0.0220 AC XY: 1636AN XY: 74412
ClinVar
Submissions by phenotype
Thrombocytopenia 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 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. - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 02, 2019 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at