2-86456416-ATTTTTTTTTTTT-ATTTTTTTTTTTTTTTT
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_018433.6(KDM3A):c.557-7_557-4dupTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000024 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00064 ( 0 hom. )
Consequence
KDM3A
NM_018433.6 splice_region, intron
NM_018433.6 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.593
Publications
1 publications found
Genes affected
KDM3A (HGNC:20815): (lysine demethylase 3A) Enables androgen receptor binding activity; histone H3-methyl-lysine-9 demethylase activity; and iron ion binding activity. Involved in several processes, including androgen receptor signaling pathway; formaldehyde biosynthetic process; and histone H3-K9 demethylation. Located in nucleoplasm. Implicated in cervical cancer and colon cancer. Biomarker of Ewing sarcoma; hepatocellular carcinoma; nasopharynx carcinoma; and prostate cancer. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_018433.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| KDM3A | NM_018433.6 | MANE Select | c.557-7_557-4dupTTTT | splice_region intron | N/A | NP_060903.2 | |||
| KDM3A | NM_001146688.2 | c.557-7_557-4dupTTTT | splice_region intron | N/A | NP_001140160.1 | Q9Y4C1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| KDM3A | ENST00000312912.10 | TSL:1 MANE Select | c.557-26_557-25insTTTT | intron | N/A | ENSP00000323659.5 | Q9Y4C1 | ||
| KDM3A | ENST00000409064.5 | TSL:1 | c.557-26_557-25insTTTT | intron | N/A | ENSP00000386516.1 | Q9Y4C1 | ||
| KDM3A | ENST00000900202.1 | c.557-26_557-25insTTTT | intron | N/A | ENSP00000570261.1 |
Frequencies
GnomAD3 genomes 0.0000242 AC: 3AN: 124184Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
3
AN:
124184
Hom.:
Cov.:
0
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: 0.000638 AC: 595AN: 932712Hom.: 0 Cov.: 0 AF XY: 0.000665 AC XY: 307AN XY: 461732 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
595
AN:
932712
Hom.:
Cov.:
0
AF XY:
AC XY:
307
AN XY:
461732
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
16
AN:
18286
American (AMR)
AF:
AC:
14
AN:
11282
Ashkenazi Jewish (ASJ)
AF:
AC:
22
AN:
15214
East Asian (EAS)
AF:
AC:
19
AN:
24008
South Asian (SAS)
AF:
AC:
79
AN:
43386
European-Finnish (FIN)
AF:
AC:
56
AN:
35782
Middle Eastern (MID)
AF:
AC:
3
AN:
2664
European-Non Finnish (NFE)
AF:
AC:
365
AN:
743658
Other (OTH)
AF:
AC:
21
AN:
38432
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.304
Heterozygous variant carriers
0
50
100
150
200
250
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
10
20
30
40
50
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
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>80
Age
GnomAD4 genome 0.0000242 AC: 3AN: 124168Hom.: 0 Cov.: 0 AF XY: 0.0000344 AC XY: 2AN XY: 58214 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
3
AN:
124168
Hom.:
Cov.:
0
AF XY:
AC XY:
2
AN XY:
58214
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1
AN:
32462
American (AMR)
AF:
AC:
1
AN:
11952
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3206
East Asian (EAS)
AF:
AC:
0
AN:
4310
South Asian (SAS)
AF:
AC:
0
AN:
3888
European-Finnish (FIN)
AF:
AC:
0
AN:
4512
Middle Eastern (MID)
AF:
AC:
0
AN:
230
European-Non Finnish (NFE)
AF:
AC:
1
AN:
61112
Other (OTH)
AF:
AC:
0
AN:
1652
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.0000647710), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.292
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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