rs76903503
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_173551.5(ANKS6):c.330C>T(p.Tyr110=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,412,228 control chromosomes in the GnomAD database, including 10,695 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.11 ( 1097 hom., cov: 33)
Exomes 𝑓: 0.12 ( 9598 hom. )
Consequence
ANKS6
NM_173551.5 synonymous
NM_173551.5 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 1.94
Genes affected
ANKS6 (HGNC:26724): (ankyrin repeat and sterile alpha motif domain containing 6) This gene encodes a protein containing multiple ankyrin repeats and a SAM domain. It is thought that this protein may localize to the proximal region of the primary cilium, and may play a role in renal and cardiovascular development. Mutations in this gene have been shown to cause a form of nephronophthisis (NPHP16), a chronic tubulo-interstitial nephritis. [provided by RefSeq, Jul 2015]
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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=-0.53).
BP6
?
Variant 9-98796162-G-A is Benign according to our data. Variant chr9-98796162-G-A is described in ClinVar as [Benign]. Clinvar id is 262851.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=1.94 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKS6 | NM_173551.5 | c.330C>T | p.Tyr110= | synonymous_variant | 1/15 | ENST00000353234.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKS6 | ENST00000353234.5 | c.330C>T | p.Tyr110= | synonymous_variant | 1/15 | 1 | NM_173551.5 | P1 | |
ANKS6 | ENST00000375019.6 | c.-42+522C>T | intron_variant | 5 | |||||
ANKS6 | ENST00000471846.1 | n.378C>T | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.106 AC: 16112AN: 151990Hom.: 1095 Cov.: 33
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GnomAD3 exomes AF: 0.141 AC: 7877AN: 55872Hom.: 652 AF XY: 0.137 AC XY: 4479AN XY: 32698
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GnomAD4 exome AF: 0.119 AC: 149385AN: 1260130Hom.: 9598 Cov.: 30 AF XY: 0.119 AC XY: 73681AN XY: 618334
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GnomAD4 genome ? AF: 0.106 AC: 16118AN: 152098Hom.: 1097 Cov.: 33 AF XY: 0.111 AC XY: 8259AN XY: 74354
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Nephronophthisis 16 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
ANKS6-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 26, 2022 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
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