rs141939315
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_020987.5(ANK3):c.13106G>A(p.Arg4369Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00637 in 1,613,858 control chromosomes in the GnomAD database, including 54 homozygotes. In-silico tool predicts 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. R4369W) has been classified as Uncertain significance.
Frequency
Consequence
NM_020987.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANK3 | NM_020987.5 | c.13106G>A | p.Arg4369Gln | missense_variant | 43/44 | ENST00000280772.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANK3 | ENST00000280772.7 | c.13106G>A | p.Arg4369Gln | missense_variant | 43/44 | 1 | NM_020987.5 |
Frequencies
GnomAD3 genomes AF: 0.00520 AC: 791AN: 151972Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00573 AC: 1441AN: 251412Hom.: 10 AF XY: 0.00589 AC XY: 801AN XY: 135886
GnomAD4 exome AF: 0.00649 AC: 9490AN: 1461768Hom.: 51 Cov.: 30 AF XY: 0.00658 AC XY: 4784AN XY: 727194
GnomAD4 genome AF: 0.00519 AC: 790AN: 152090Hom.: 3 Cov.: 33 AF XY: 0.00485 AC XY: 361AN XY: 74372
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | ANK3: BP4, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 14, 2016 | - - |
Intellectual disability-hypotonia-spasticity-sleep disorder syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 19, 2022 | - - |
ANK3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 26, 2021 | 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