rs115903343
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000280772.7(ANK3):āc.10953A>Cā(p.Lys3651Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00199 in 1,614,014 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
ENST00000280772.7 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANK3 | NM_020987.5 | c.10953A>C | p.Lys3651Asn | missense_variant | 37/44 | ENST00000280772.7 | NP_066267.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANK3 | ENST00000280772.7 | c.10953A>C | p.Lys3651Asn | missense_variant | 37/44 | 1 | NM_020987.5 | ENSP00000280772 |
Frequencies
GnomAD3 genomes AF: 0.00998 AC: 1518AN: 152162Hom.: 29 Cov.: 32
GnomAD3 exomes AF: 0.00290 AC: 727AN: 251050Hom.: 12 AF XY: 0.00204 AC XY: 277AN XY: 135696
GnomAD4 exome AF: 0.00115 AC: 1681AN: 1461734Hom.: 19 Cov.: 34 AF XY: 0.000976 AC XY: 710AN XY: 727162
GnomAD4 genome AF: 0.0100 AC: 1529AN: 152280Hom.: 29 Cov.: 32 AF XY: 0.00972 AC XY: 724AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 03, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 18, 2024 | - - |
ANK3-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2020 | 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