rs201904871
Positions:
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_173551.5(ANKS6):āc.1458T>Cā(p.Pro486=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000805 in 1,614,184 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 (ā ā ).
Frequency
Genomes: š 0.00049 ( 0 hom., cov: 32)
Exomes š: 0.00084 ( 2 hom. )
Consequence
ANKS6
NM_173551.5 synonymous
NM_173551.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.352
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
?
Variant 9-98778335-A-G is Benign according to our data. Variant chr9-98778335-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 262841.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-98778335-A-G is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=0.352 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.1458T>C | p.Pro486= | synonymous_variant | 7/15 | ENST00000353234.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKS6 | ENST00000353234.5 | c.1458T>C | p.Pro486= | synonymous_variant | 7/15 | 1 | NM_173551.5 | P1 | |
ANKS6 | ENST00000375019.6 | c.555T>C | p.Pro185= | synonymous_variant | 6/15 | 5 | |||
ANKS6 | ENST00000634393.1 | n.558T>C | non_coding_transcript_exon_variant | 5/15 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000486 AC: 74AN: 152188Hom.: 0 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
74
AN:
152188
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000477 AC: 119AN: 249464Hom.: 0 AF XY: 0.000517 AC XY: 70AN XY: 135386
GnomAD3 exomes
AF:
AC:
119
AN:
249464
Hom.:
AF XY:
AC XY:
70
AN XY:
135386
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000838 AC: 1225AN: 1461878Hom.: 2 Cov.: 31 AF XY: 0.000822 AC XY: 598AN XY: 727238
GnomAD4 exome
AF:
AC:
1225
AN:
1461878
Hom.:
Cov.:
31
AF XY:
AC XY:
598
AN XY:
727238
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000486 AC: 74AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000416 AC XY: 31AN XY: 74474
GnomAD4 genome
?
AF:
AC:
74
AN:
152306
Hom.:
Cov.:
32
AF XY:
AC XY:
31
AN XY:
74474
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:4
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 | Apr 20, 2022 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2023 | ANKS6: BP4, BP7 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at