rs147726863
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_013275.6(ANKRD11):āc.5661A>Gā(p.Gln1887Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00179 in 1,604,154 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.0017 ( 3 hom., cov: 32)
Exomes š: 0.0018 ( 5 hom. )
Consequence
ANKRD11
NM_013275.6 synonymous
NM_013275.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.963
Genes affected
ANKRD11 (HGNC:21316): (ankyrin repeat domain containing 11) This locus encodes an ankryin repeat domain-containing protein. The encoded protein inhibits ligand-dependent activation of transcription. Mutations in this gene have been associated with KBG syndrome, which is characterized by macrodontia, distinctive craniofacial features, short stature, skeletal anomalies, global developmental delay, seizures and intellectual disability. Alternatively spliced transcript variants have been described. Related pseudogenes exist on chromosomes 2 and X. [provided by RefSeq, Jan 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant 16-89280881-T-C is Benign according to our data. Variant chr16-89280881-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 210180.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.963 with no splicing effect.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00169 (258/152272) while in subpopulation AMR AF= 0.003 (46/15310). AF 95% confidence interval is 0.00231. There are 3 homozygotes in gnomad4. There are 122 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 258 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANKRD11 | NM_013275.6 | c.5661A>G | p.Gln1887Gln | synonymous_variant | 9/13 | ENST00000301030.10 | NP_037407.4 | |
ANKRD11 | NM_001256182.2 | c.5661A>G | p.Gln1887Gln | synonymous_variant | 10/14 | NP_001243111.1 | ||
ANKRD11 | NM_001256183.2 | c.5661A>G | p.Gln1887Gln | synonymous_variant | 9/13 | NP_001243112.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANKRD11 | ENST00000301030.10 | c.5661A>G | p.Gln1887Gln | synonymous_variant | 9/13 | 5 | NM_013275.6 | ENSP00000301030.4 |
Frequencies
GnomAD3 genomes AF: 0.00170 AC: 258AN: 152156Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00144 AC: 358AN: 248406Hom.: 0 AF XY: 0.00150 AC XY: 202AN XY: 134340
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GnomAD4 exome AF: 0.00180 AC: 2620AN: 1451882Hom.: 5 Cov.: 34 AF XY: 0.00181 AC XY: 1304AN XY: 720292
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GnomAD4 genome AF: 0.00169 AC: 258AN: 152272Hom.: 3 Cov.: 32 AF XY: 0.00164 AC XY: 122AN XY: 74450
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
KBG syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 19, 2024 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2024 | ANKRD11: BP4, BP7 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 17, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 25, 2016 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 21, 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. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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