16-89268526-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_013275.6(ANKRD11):c.7944C>T(p.Tyr2648=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000756 in 1,454,934 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 29)
Exomes 𝑓: 0.0000061 ( 0 hom. )
Consequence
ANKRD11
NM_013275.6 synonymous
NM_013275.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.180
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
?
Variant 16-89268526-G-A is Benign according to our data. Variant chr16-89268526-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1761334.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.18 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKRD11 | NM_013275.6 | c.7944C>T | p.Tyr2648= | synonymous_variant | 13/13 | ENST00000301030.10 | |
ANKRD11 | NM_001256182.2 | c.7944C>T | p.Tyr2648= | synonymous_variant | 14/14 | ||
ANKRD11 | NM_001256183.2 | c.7944C>T | p.Tyr2648= | synonymous_variant | 13/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKRD11 | ENST00000301030.10 | c.7944C>T | p.Tyr2648= | synonymous_variant | 13/13 | 5 | NM_013275.6 | P1 | |
ENST00000602042.1 | n.423G>A | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000202 AC: 3AN: 148414Hom.: 0 Cov.: 29
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GnomAD3 exomes AF: 0.00000654 AC: 1AN: 152848Hom.: 0 AF XY: 0.0000122 AC XY: 1AN XY: 81652
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GnomAD4 exome AF: 0.00000612 AC: 8AN: 1306520Hom.: 0 Cov.: 20 AF XY: 0.00000464 AC XY: 3AN XY: 647050
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
KBG syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 01, 2022 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 29, 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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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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