rs10821729
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000280772.7(ANK3):c.114+50010G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,956 control chromosomes in the GnomAD database, including 19,693 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.50 ( 19693 hom., cov: 32)
Consequence
ANK3
ENST00000280772.7 intron
ENST00000280772.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.65
Genes affected
ANK3 (HGNC:494): (ankyrin 3) Ankyrins are a family of proteins that are believed to link the integral membrane proteins to the underlying spectrin-actin cytoskeleton and play key roles in activities such as cell motility, activation, proliferation, contact, and the maintenance of specialized membrane domains. Multiple isoforms of ankyrin with different affinities for various target proteins are expressed in a tissue-specific, developmentally regulated manner. Most ankyrins are typically composed of three structural domains: an amino-terminal domain containing multiple ankyrin repeats; a central region with a highly conserved spectrin binding domain; and a carboxy-terminal regulatory domain which is the least conserved and subject to variation. Ankyrin 3 is an immunologically distinct gene product from ankyrins 1 and 2, and was originally found at the axonal initial segment and nodes of Ranvier of neurons in the central and peripheral nervous systems. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANK3 | NM_020987.5 | c.114+50010G>A | intron_variant | ENST00000280772.7 | NP_066267.2 | |||
ANK3 | NM_001204403.2 | c.97-59776G>A | intron_variant | NP_001191332.1 | ||||
ANK3 | NM_001204404.2 | c.64-59776G>A | intron_variant | NP_001191333.1 | ||||
ANK3 | NM_001320874.2 | c.114+50010G>A | intron_variant | NP_001307803.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANK3 | ENST00000280772.7 | c.114+50010G>A | intron_variant | 1 | NM_020987.5 | ENSP00000280772 |
Frequencies
GnomAD3 genomes AF: 0.502 AC: 76230AN: 151836Hom.: 19678 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.502 AC: 76284AN: 151956Hom.: 19693 Cov.: 32 AF XY: 0.512 AC XY: 38024AN XY: 74278
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2171
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3478
ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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