16-89279755-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_013275.6(ANKRD11):c.6787C>T(p.Pro2263Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0382 in 1,523,960 control chromosomes in the GnomAD database, including 1,391 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_013275.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKRD11 | NM_013275.6 | c.6787C>T | p.Pro2263Ser | missense_variant | 9/13 | ENST00000301030.10 | |
ANKRD11 | NM_001256182.2 | c.6787C>T | p.Pro2263Ser | missense_variant | 10/14 | ||
ANKRD11 | NM_001256183.2 | c.6787C>T | p.Pro2263Ser | missense_variant | 9/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKRD11 | ENST00000301030.10 | c.6787C>T | p.Pro2263Ser | missense_variant | 9/13 | 5 | NM_013275.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0337 AC: 5121AN: 152136Hom.: 150 Cov.: 32
GnomAD3 exomes AF: 0.0331 AC: 4156AN: 125568Hom.: 123 AF XY: 0.0313 AC XY: 2157AN XY: 68946
GnomAD4 exome AF: 0.0387 AC: 53029AN: 1371706Hom.: 1241 Cov.: 33 AF XY: 0.0376 AC XY: 25397AN XY: 675234
GnomAD4 genome AF: 0.0336 AC: 5122AN: 152254Hom.: 150 Cov.: 32 AF XY: 0.0375 AC XY: 2788AN XY: 74444
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 22, 2015 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 28, 2017 | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
KBG syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 18, 2016 | This alteration is classified as 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. - |
not provided Benign:1
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at