NM_015158.5:c.*178A>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_015158.5(KANK1):c.*178A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 637,140 control chromosomes in the GnomAD database, including 146,563 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.71 ( 39609 hom., cov: 30)
Exomes 𝑓: 0.66 ( 106954 hom. )
Consequence
KANK1
NM_015158.5 3_prime_UTR
NM_015158.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.69
Publications
11 publications found
Genes affected
KANK1 (HGNC:19309): (KN motif and ankyrin repeat domains 1) The protein encoded by this gene belongs to the Kank family of proteins, which contain multiple ankyrin repeat domains. This family member functions in cytoskeleton formation by regulating actin polymerization. This gene is a candidate tumor suppressor for renal cell carcinoma. Mutations in this gene cause cerebral palsy spastic quadriplegic type 2, a central nervous system development disorder. A t(5;9) translocation results in fusion of the platelet-derived growth factor receptor beta gene (PDGFRB) on chromosome 5 with this gene in a myeloproliferative neoplasm featuring severe thrombocythemia. Alternative splicing of this gene results in multiple transcript variants. A related pseudogene has been identified on chromosome 20. [provided by RefSeq, Dec 2014]
KANK1 Gene-Disease associations (from GenCC):
- spastic quadriplegic cerebral palsyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- cerebral palsy, spastic quadriplegic, 2Inheritance: Unknown, AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 9-745413-A-G is Benign according to our data. Variant chr9-745413-A-G is described in ClinVar as Benign. ClinVar VariationId is 1278047.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.714 AC: 108435AN: 151854Hom.: 39563 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
108435
AN:
151854
Hom.:
Cov.:
30
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:
GnomAD4 exome AF: 0.659 AC: 319918AN: 485168Hom.: 106954 Cov.: 7 AF XY: 0.658 AC XY: 167877AN XY: 255102 show subpopulations
GnomAD4 exome
AF:
AC:
319918
AN:
485168
Hom.:
Cov.:
7
AF XY:
AC XY:
167877
AN XY:
255102
show subpopulations
African (AFR)
AF:
AC:
11049
AN:
12626
American (AMR)
AF:
AC:
13145
AN:
20076
Ashkenazi Jewish (ASJ)
AF:
AC:
7960
AN:
13256
East Asian (EAS)
AF:
AC:
14198
AN:
27636
South Asian (SAS)
AF:
AC:
30267
AN:
46628
European-Finnish (FIN)
AF:
AC:
20535
AN:
32150
Middle Eastern (MID)
AF:
AC:
1436
AN:
2112
European-Non Finnish (NFE)
AF:
AC:
203953
AN:
304876
Other (OTH)
AF:
AC:
17375
AN:
25808
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
5042
10083
15125
20166
25208
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
2054
4108
6162
8216
10270
<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: 0.714 AC: 108530AN: 151972Hom.: 39609 Cov.: 30 AF XY: 0.708 AC XY: 52589AN XY: 74270 show subpopulations
GnomAD4 genome
AF:
AC:
108530
AN:
151972
Hom.:
Cov.:
30
AF XY:
AC XY:
52589
AN XY:
74270
show subpopulations
African (AFR)
AF:
AC:
36346
AN:
41466
American (AMR)
AF:
AC:
9525
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
AC:
2151
AN:
3472
East Asian (EAS)
AF:
AC:
2982
AN:
5136
South Asian (SAS)
AF:
AC:
3063
AN:
4816
European-Finnish (FIN)
AF:
AC:
6553
AN:
10554
Middle Eastern (MID)
AF:
AC:
216
AN:
292
European-Non Finnish (NFE)
AF:
AC:
45589
AN:
67956
Other (OTH)
AF:
AC:
1454
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1481
2962
4442
5923
7404
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
826
1652
2478
3304
4130
<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:
1937
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Nov 12, 2018
GeneDx
Significance: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
RBP_binding_hub_radar
RBP_regulation_power_radar
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
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