rs200724087
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_013275.6(ANKRD11):āc.6112A>Gā(p.Lys2038Glu) variant causes a missense change. The variant allele was found at a frequency of 0.000827 in 1,579,448 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K2038T) has been classified as Likely benign.
Frequency
Consequence
NM_013275.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKRD11 | NM_013275.6 | c.6112A>G | p.Lys2038Glu | missense_variant | 9/13 | ENST00000301030.10 | |
ANKRD11 | NM_001256182.2 | c.6112A>G | p.Lys2038Glu | missense_variant | 10/14 | ||
ANKRD11 | NM_001256183.2 | c.6112A>G | p.Lys2038Glu | missense_variant | 9/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKRD11 | ENST00000301030.10 | c.6112A>G | p.Lys2038Glu | missense_variant | 9/13 | 5 | NM_013275.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000533 AC: 81AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000626 AC: 124AN: 198090Hom.: 0 AF XY: 0.000799 AC XY: 88AN XY: 110076
GnomAD4 exome AF: 0.000859 AC: 1226AN: 1427222Hom.: 3 Cov.: 34 AF XY: 0.000942 AC XY: 665AN XY: 706296
GnomAD4 genome ? AF: 0.000526 AC: 80AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.000497 AC XY: 37AN XY: 74434
ClinVar
Submissions by phenotype
KBG syndrome Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 01, 2022 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Oct 27, 2023 | - - |
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2023 | ANKRD11: BP4, BS1 - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Mar 09, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 14, 2020 | This variant is associated with the following publications: (PMID: 28529015) - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 25, 2017 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
ANKRD11-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 24, 2020 | This variant is classified as likely 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