NM_173551.5:c.*17C>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_173551.5(ANKS6):c.*17C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000394 in 1,598,052 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000039 ( 0 hom. )
Consequence
ANKS6
NM_173551.5 3_prime_UTR
NM_173551.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0220
Publications
0 publications found
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]
ANKS6 Gene-Disease associations (from GenCC):
- nephronophthisis 16Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae)
- nephronophthisis 1Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- nephronophthisis 2Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 9-98736502-G-T is Benign according to our data. Variant chr9-98736502-G-T is described in ClinVar as Likely_benign. ClinVar VariationId is 262836.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANKS6 | ENST00000353234.5 | c.*17C>A | 3_prime_UTR_variant | Exon 15 of 15 | 1 | NM_173551.5 | ENSP00000297837.6 | |||
ANKS6 | ENST00000444472.5 | c.*17C>A | 3_prime_UTR_variant | Exon 8 of 9 | 2 | ENSP00000398648.1 | ||||
ANKS6 | ENST00000375019.6 | c.1705+25C>A | intron_variant | Intron 14 of 14 | 5 | ENSP00000364159.2 | ||||
ANKS6 | ENST00000634393.1 | n.1743+25C>A | intron_variant | Intron 14 of 14 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152188Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
6
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:
GnomAD2 exomes AF: 0.0000594 AC: 14AN: 235772 AF XY: 0.0000705 show subpopulations
GnomAD2 exomes
AF:
AC:
14
AN:
235772
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000394 AC: 57AN: 1445864Hom.: 0 Cov.: 32 AF XY: 0.0000307 AC XY: 22AN XY: 716900 show subpopulations
GnomAD4 exome
AF:
AC:
57
AN:
1445864
Hom.:
Cov.:
32
AF XY:
AC XY:
22
AN XY:
716900
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33160
American (AMR)
AF:
AC:
1
AN:
43582
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25494
East Asian (EAS)
AF:
AC:
13
AN:
39334
South Asian (SAS)
AF:
AC:
0
AN:
83958
European-Finnish (FIN)
AF:
AC:
0
AN:
52798
Middle Eastern (MID)
AF:
AC:
0
AN:
5706
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1102100
Other (OTH)
AF:
AC:
42
AN:
59732
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
5
10
14
19
24
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74342 show subpopulations
GnomAD4 genome
AF:
AC:
6
AN:
152188
Hom.:
Cov.:
32
AF XY:
AC XY:
2
AN XY:
74342
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41444
American (AMR)
AF:
AC:
0
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
6
AN:
5190
South Asian (SAS)
AF:
AC:
0
AN:
4822
European-Finnish (FIN)
AF:
AC:
0
AN:
10616
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68044
Other (OTH)
AF:
AC:
0
AN:
2094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
10
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
-
PreventionGenetics, part of Exact Sciences
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Nephronophthisis 16 Benign:1
Feb 06, 2024
Fulgent Genetics, Fulgent Genetics
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.