chr16-89268198-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_013275.6(ANKRD11):c.*280C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0056 ( 1 hom., cov: 11)
Exomes 𝑓: 0.0069 ( 2 hom. )
Failed GnomAD Quality Control
Consequence
ANKRD11
NM_013275.6 3_prime_UTR
NM_013275.6 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.18
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BP6
?
Variant 16-89268198-G-C is Benign according to our data. Variant chr16-89268198-G-C is described in ClinVar as [Benign]. Clinvar id is 1273107.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.00687 (644/93788) while in subpopulation NFE AF= 0.0097 (547/56378). AF 95% confidence interval is 0.00903. There are 2 homozygotes in gnomad4_exome. There are 293 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
?
High AC in GnomAdExome at 124 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKRD11 | NM_013275.6 | c.*280C>G | 3_prime_UTR_variant | 13/13 | ENST00000301030.10 | ||
ANKRD11 | NM_001256182.2 | c.*280C>G | 3_prime_UTR_variant | 14/14 | |||
ANKRD11 | NM_001256183.2 | c.*280C>G | 3_prime_UTR_variant | 13/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKRD11 | ENST00000301030.10 | c.*280C>G | 3_prime_UTR_variant | 13/13 | 5 | NM_013275.6 | P1 | ||
ENST00000602042.1 | n.95G>C | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 533AN: 95530Hom.: 1 Cov.: 11 FAILED QC
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GnomAD3 exomes AF: 0.00516 AC: 124AN: 24008Hom.: 0 AF XY: 0.00457 AC XY: 58AN XY: 12682
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GnomAD4 exome AF: 0.00687 AC: 644AN: 93788Hom.: 2 Cov.: 0 AF XY: 0.00592 AC XY: 293AN XY: 49454
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.00557 AC: 533AN: 95608Hom.: 1 Cov.: 11 AF XY: 0.00549 AC XY: 229AN XY: 41686
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 04, 2020 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at