rs137870160
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_173551.5(ANKS6):c.603C>T(p.His201=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000458 in 1,613,484 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 0.0025 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00024 ( 1 hom. )
Consequence
ANKS6
NM_173551.5 synonymous
NM_173551.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.91
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 9-98790363-G-A is Benign according to our data. Variant chr9-98790363-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 541405.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-1.91 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKS6 | NM_173551.5 | c.603C>T | p.His201= | synonymous_variant | 2/15 | ENST00000353234.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKS6 | ENST00000353234.5 | c.603C>T | p.His201= | synonymous_variant | 2/15 | 1 | NM_173551.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00248 AC: 377AN: 152214Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000658 AC: 162AN: 246038Hom.: 2 AF XY: 0.000537 AC XY: 72AN XY: 133978
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GnomAD4 exome AF: 0.000244 AC: 356AN: 1461152Hom.: 1 Cov.: 31 AF XY: 0.000201 AC XY: 146AN XY: 726912
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GnomAD4 genome ? AF: 0.00251 AC: 383AN: 152332Hom.: 1 Cov.: 32 AF XY: 0.00240 AC XY: 179AN XY: 74480
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Nephronophthisis 16 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 11, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
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