rs397517250
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
The NM_014391.3(ANKRD1):c.346-17_346-10del 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 0.0189 in 1,269,304 control chromosomes in the GnomAD database, including 3,441 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.0059 ( 7 hom., cov: 0)
Exomes 𝑓: 0.020 ( 3434 hom. )
Consequence
ANKRD1
NM_014391.3 splice_polypyrimidine_tract, intron
NM_014391.3 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.19
Genes affected
ANKRD1 (HGNC:15819): (ankyrin repeat domain 1) The protein encoded by this gene is localized to the nucleus of endothelial cells and is induced by IL-1 and TNF-alpha stimulation. Studies in rat cardiomyocytes suggest that this gene functions as a transcription factor. Interactions between this protein and the sarcomeric proteins myopalladin and titin suggest that it may also be involved in the myofibrillar stretch-sensor system. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP6
Variant 10-90918981-AAAATAAAT-A is Benign according to our data. Variant chr10-90918981-AAAATAAAT-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 45631.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Benign=4, Uncertain_significance=1}. Variant chr10-90918981-AAAATAAAT-A is described in Lovd as [Benign].
BA1
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANKRD1 | NM_014391.3 | c.346-17_346-10del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000371697.4 | NP_055206.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANKRD1 | ENST00000371697.4 | c.346-17_346-10del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_014391.3 | ENSP00000360762 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00587 AC: 524AN: 89238Hom.: 7 Cov.: 0
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GnomAD4 exome AF: 0.0199 AC: 23458AN: 1180070Hom.: 3434 AF XY: 0.0206 AC XY: 12232AN XY: 592942
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GnomAD4 genome AF: 0.00588 AC: 525AN: 89234Hom.: 7 Cov.: 0 AF XY: 0.00604 AC XY: 258AN XY: 42742
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:7
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Congenital total pulmonary venous return anomaly Benign:3
Benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Oct 11, 2017 | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | Oct 26, 2016 | - - |
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 20, 2013 | The c.346-17_346-10del variant in ANKRD1 has not been reported in the literature nor previously identified by our laboratory. This variant is located in a rep etitive region in intron 3 that contains several other common deletions and has been detected in 2/100 control chromosomes tested by our laboratory. Based on t he overall evidence for variants affecting this region and its frequency in cont rols this variant is likely benign. - |
Dilated Cardiomyopathy, Dominant Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Cardiomyopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 08, 2013 | The variant is found in DCM panel(s). - |
ANKRD1-related dilated cardiomyopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 19, 2024 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at