rs141868637
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_173551.5(ANKS6):c.1740C>T(p.Asn580=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000389 in 1,602,476 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0018 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00024 ( 2 hom. )
Consequence
ANKS6
NM_173551.5 synonymous
NM_173551.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.86
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 -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 9-98773958-G-A is Benign according to our data. Variant chr9-98773958-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 262844.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-2.86 with no splicing effect.
BS2
?
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKS6 | NM_173551.5 | c.1740C>T | p.Asn580= | synonymous_variant | 9/15 | ENST00000353234.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKS6 | ENST00000353234.5 | c.1740C>T | p.Asn580= | synonymous_variant | 9/15 | 1 | NM_173551.5 | P1 | |
ANKS6 | ENST00000375019.6 | c.837C>T | p.Asn279= | synonymous_variant | 8/15 | 5 | |||
ANKS6 | ENST00000444472.5 | c.147C>T | p.Asn49= | synonymous_variant | 2/9 | 2 | |||
ANKS6 | ENST00000634393.1 | n.840C>T | non_coding_transcript_exon_variant | 7/15 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00181 AC: 274AN: 151796Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000475 AC: 113AN: 237828Hom.: 0 AF XY: 0.000340 AC XY: 44AN XY: 129486
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GnomAD4 exome AF: 0.000239 AC: 347AN: 1450562Hom.: 2 Cov.: 32 AF XY: 0.000220 AC XY: 159AN XY: 721616
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Nephronophthisis 16 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 06, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | ANKS6: BP4, BP7 - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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