NM_015245.3:c.2011-13198G>C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015245.3(ANKS1A):c.2011-13198G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,220 control chromosomes in the GnomAD database, including 2,439 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.17 ( 2439 hom., cov: 32)
Consequence
ANKS1A
NM_015245.3 intron
NM_015245.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.992
Publications
10 publications found
Genes affected
ANKS1A (HGNC:20961): (ankyrin repeat and sterile alpha motif domain containing 1A) Predicted to enable ephrin receptor binding activity. Predicted to be involved in ephrin receptor signaling pathway; neuron remodeling; and substrate-dependent cell migration. Predicted to act upstream of or within negative regulation of ubiquitin-dependent protein catabolic process and regulation of ephrin receptor signaling pathway. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANKS1A | ENST00000360359.5 | c.2011-13198G>C | intron_variant | Intron 11 of 23 | 1 | NM_015245.3 | ENSP00000353518.3 | |||
ANKS1A | ENST00000649117.1 | c.2074-13198G>C | intron_variant | Intron 12 of 24 | ENSP00000497393.1 | |||||
ENSG00000286550 | ENST00000660796.1 | n.*215C>G | downstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.168 AC: 25612AN: 152102Hom.: 2432 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
25612
AN:
152102
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.168 AC: 25632AN: 152220Hom.: 2439 Cov.: 32 AF XY: 0.164 AC XY: 12193AN XY: 74426 show subpopulations
GnomAD4 genome
AF:
AC:
25632
AN:
152220
Hom.:
Cov.:
32
AF XY:
AC XY:
12193
AN XY:
74426
show subpopulations
African (AFR)
AF:
AC:
4661
AN:
41550
American (AMR)
AF:
AC:
2603
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
AC:
234
AN:
3472
East Asian (EAS)
AF:
AC:
110
AN:
5176
South Asian (SAS)
AF:
AC:
673
AN:
4822
European-Finnish (FIN)
AF:
AC:
2025
AN:
10588
Middle Eastern (MID)
AF:
AC:
17
AN:
294
European-Non Finnish (NFE)
AF:
AC:
14909
AN:
67998
Other (OTH)
AF:
AC:
272
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1073
2146
3220
4293
5366
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
282
564
846
1128
1410
<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:
436
AN:
3478
ClinVar
Not reported inComputational 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
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