11-67231384-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012308.3(KDM2A):c.1085-182T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 152,046 control chromosomes in the GnomAD database, including 45,968 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 0.73 ( 45968 hom., cov: 30)
Consequence
KDM2A
NM_012308.3 intron
NM_012308.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.167
Publications
7 publications found
Genes affected
KDM2A (HGNC:13606): (lysine demethylase 2A) This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbls class and, in addition to an F-box, contains at least six highly degenerated leucine-rich repeats. This family member plays a role in epigenetic silencing. It nucleates at CpG islands and specifically demethylates both mono- and di-methylated lysine-36 of histone H3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]
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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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.727 AC: 110376AN: 151928Hom.: 45971 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
110376
AN:
151928
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.726 AC: 110389AN: 152046Hom.: 45968 Cov.: 30 AF XY: 0.729 AC XY: 54161AN XY: 74326 show subpopulations
GnomAD4 genome
AF:
AC:
110389
AN:
152046
Hom.:
Cov.:
30
AF XY:
AC XY:
54161
AN XY:
74326
show subpopulations
African (AFR)
AF:
AC:
12370
AN:
41426
American (AMR)
AF:
AC:
10521
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
3282
AN:
3470
East Asian (EAS)
AF:
AC:
3967
AN:
5160
South Asian (SAS)
AF:
AC:
4503
AN:
4822
European-Finnish (FIN)
AF:
AC:
9428
AN:
10584
Middle Eastern (MID)
AF:
AC:
256
AN:
292
European-Non Finnish (NFE)
AF:
AC:
63546
AN:
68002
Other (OTH)
AF:
AC:
1641
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
919
1838
2756
3675
4594
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
794
1588
2382
3176
3970
<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:
2703
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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