chr16-89284698-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_013275.6(ANKRD11):c.1844C>G(p.Ala615Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00126 in 1,613,834 control chromosomes in the GnomAD database, including 26 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 Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A615T) 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 -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKRD11 | NM_013275.6 | c.1844C>G | p.Ala615Gly | missense_variant | 9/13 | ENST00000301030.10 | |
ANKRD11 | NM_001256182.2 | c.1844C>G | p.Ala615Gly | missense_variant | 10/14 | ||
ANKRD11 | NM_001256183.2 | c.1844C>G | p.Ala615Gly | missense_variant | 9/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKRD11 | ENST00000301030.10 | c.1844C>G | p.Ala615Gly | missense_variant | 9/13 | 5 | NM_013275.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00694 AC: 1055AN: 152058Hom.: 13 Cov.: 32
GnomAD3 exomes AF: 0.00173 AC: 431AN: 249500Hom.: 6 AF XY: 0.00137 AC XY: 186AN XY: 135456
GnomAD4 exome AF: 0.000672 AC: 982AN: 1461658Hom.: 13 Cov.: 37 AF XY: 0.000594 AC XY: 432AN XY: 727146
GnomAD4 genome ? AF: 0.00696 AC: 1059AN: 152176Hom.: 13 Cov.: 32 AF XY: 0.00683 AC XY: 508AN XY: 74394
ClinVar
Submissions by phenotype
KBG syndrome Benign:3
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 13, 2022 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 11, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Oct 25, 2017 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 04, 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at