2-86456416-ATTTTTTTTTTTT-ATTTTTTTTTTTTTTT
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP6BS2
The NM_018433.6(KDM3A):c.557-6_557-4dupTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.00020 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0061 ( 1 hom. )
Consequence
KDM3A
NM_018433.6 splice_region, intron
NM_018433.6 splice_region, intron
Scores
Not classified
Clinical Significance
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: Likely_benign. The variant received -5 ACMG points.
BP6
Variant 2-86456416-A-ATTT is Benign according to our data. Variant chr2-86456416-A-ATTT is described in ClinVar as Benign. ClinVar VariationId is 3049186.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High AC in GnomAd4 at 25 AD gene.
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.557-6_557-4dupTTT | splice_region intron | N/A | NP_060903.2 | |||
| KDM3A | NM_001146688.2 | c.557-6_557-4dupTTT | 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_557-25insTTT | intron | N/A | ENSP00000323659.5 | Q9Y4C1 | ||
| KDM3A | ENST00000409064.5 | TSL:1 | c.557-26_557-25insTTT | intron | N/A | ENSP00000386516.1 | Q9Y4C1 | ||
| KDM3A | ENST00000900202.1 | c.557-26_557-25insTTT | intron | N/A | ENSP00000570261.1 |
Frequencies
GnomAD3 genomes 0.000201 AC: 25AN: 124184Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
25
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
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Gnomad NFE
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Gnomad OTH
AF:
GnomAD2 exomes AF: 0.0176 AC: 547AN: 31146 AF XY: 0.0182 show subpopulations
GnomAD2 exomes
AF:
AC:
547
AN:
31146
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
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Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00606 AC: 5625AN: 927632Hom.: 1 Cov.: 0 AF XY: 0.00630 AC XY: 2894AN XY: 459132 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
5625
AN:
927632
Hom.:
Cov.:
0
AF XY:
AC XY:
2894
AN XY:
459132
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
140
AN:
18178
American (AMR)
AF:
AC:
93
AN:
11224
Ashkenazi Jewish (ASJ)
AF:
AC:
134
AN:
15110
East Asian (EAS)
AF:
AC:
129
AN:
23900
South Asian (SAS)
AF:
AC:
561
AN:
43094
European-Finnish (FIN)
AF:
AC:
428
AN:
35436
Middle Eastern (MID)
AF:
AC:
16
AN:
2652
European-Non Finnish (NFE)
AF:
AC:
3853
AN:
739846
Other (OTH)
AF:
AC:
271
AN:
38192
⚠️ 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: 0.297
Heterozygous variant carriers
0
455
910
1364
1819
2274
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
114
228
342
456
570
<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 0.000201 AC: 25AN: 124168Hom.: 0 Cov.: 0 AF XY: 0.000172 AC XY: 10AN XY: 58218 show subpopulations
GnomAD4 genome
AF:
AC:
25
AN:
124168
Hom.:
Cov.:
0
AF XY:
AC XY:
10
AN XY:
58218
show subpopulations
African (AFR)
AF:
AC:
5
AN:
32464
American (AMR)
AF:
AC:
2
AN:
11954
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3206
East Asian (EAS)
AF:
AC:
0
AN:
4314
South Asian (SAS)
AF:
AC:
0
AN:
3888
European-Finnish (FIN)
AF:
AC:
1
AN:
4510
Middle Eastern (MID)
AF:
AC:
0
AN:
230
European-Non Finnish (NFE)
AF:
AC:
16
AN:
61108
Other (OTH)
AF:
AC:
1
AN:
1652
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.401
Heterozygous variant carriers
0
1
2
4
5
6
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
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>80
Age
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Benign
Revision:no assertion criteria provided
Pathogenic
VUS
Benign
Condition
-
-
1
KDM3A-related disorder (1)
Computational 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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