chr1-23019623-C-CGCG
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP3BP6BS2
The NM_001009999.3(KDM1A):c.39_41dupGGC(p.Ala14dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000395 in 1,418,088 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000040 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000039 ( 0 hom. )
Consequence
KDM1A
NM_001009999.3 disruptive_inframe_insertion
NM_001009999.3 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.53
Publications
0 publications found
Genes affected
KDM1A (HGNC:29079): (lysine demethylase 1A) This gene encodes a nuclear protein containing a SWIRM domain, a FAD-binding motif, and an amine oxidase domain. This protein is a component of several histone deacetylase complexes, though it silences genes by functioning as a histone demethylase. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
KDM1A Gene-Disease associations (from GenCC):
- palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndromeInheritance: AD Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -6 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001009999.3
BP6
Variant 1-23019623-C-CGCG is Benign according to our data. Variant chr1-23019623-C-CGCG is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 1675352.
BS2
High AC in GnomAd4 at 6 AD gene.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001009999.3. 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 |
|---|---|---|---|---|---|---|---|---|---|
| KDM1A | NM_001009999.3 | MANE Select | c.39_41dupGGC | p.Ala14dup | disruptive_inframe_insertion | Exon 1 of 21 | NP_001009999.1 | O60341-2 | |
| KDM1A | NM_001410762.1 | c.39_41dupGGC | p.Ala14dup | disruptive_inframe_insertion | Exon 1 of 20 | NP_001397691.1 | A0A8I5KXU4 | ||
| KDM1A | NM_001363654.2 | c.39_41dupGGC | p.Ala14dup | disruptive_inframe_insertion | Exon 1 of 19 | NP_001350583.1 | R4GMQ1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| KDM1A | ENST00000400181.9 | TSL:1 MANE Select | c.39_41dupGGC | p.Ala14dup | disruptive_inframe_insertion | Exon 1 of 21 | ENSP00000383042.5 | O60341-2 | |
| KDM1A | ENST00000356634.7 | TSL:1 | c.39_41dupGGC | p.Ala14dup | disruptive_inframe_insertion | Exon 1 of 19 | ENSP00000349049.3 | O60341-1 | |
| KDM1A | ENST00000874661.1 | c.39_41dupGGC | p.Ala14dup | disruptive_inframe_insertion | Exon 1 of 21 | ENSP00000544720.1 |
Frequencies
GnomAD3 genomes 0.0000395 AC: 6AN: 151712Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
6
AN:
151712
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
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Gnomad EAS
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Gnomad SAS
AF:
Gnomad FIN
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Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.00 AC: 0AN: 58636 AF XY: 0.00
GnomAD2 exomes
AF:
AC:
0
AN:
58636
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000395 AC: 50AN: 1266376Hom.: 0 Cov.: 31 AF XY: 0.0000369 AC XY: 23AN XY: 623036 show subpopulations
GnomAD4 exome
AF:
AC:
50
AN:
1266376
Hom.:
Cov.:
31
AF XY:
AC XY:
23
AN XY:
623036
show subpopulations
African (AFR)
AF:
AC:
0
AN:
25464
American (AMR)
AF:
AC:
2
AN:
17278
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
19726
East Asian (EAS)
AF:
AC:
0
AN:
29544
South Asian (SAS)
AF:
AC:
2
AN:
60458
European-Finnish (FIN)
AF:
AC:
0
AN:
31272
Middle Eastern (MID)
AF:
AC:
0
AN:
3552
European-Non Finnish (NFE)
AF:
AC:
40
AN:
1027244
Other (OTH)
AF:
AC:
5
AN:
51838
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.463
Heterozygous variant carriers
0
3
6
8
11
14
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
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>80
Age
GnomAD4 genome 0.0000395 AC: 6AN: 151712Hom.: 0 Cov.: 32 AF XY: 0.0000405 AC XY: 3AN XY: 74086 show subpopulations
GnomAD4 genome
AF:
AC:
6
AN:
151712
Hom.:
Cov.:
32
AF XY:
AC XY:
3
AN XY:
74086
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41382
American (AMR)
AF:
AC:
4
AN:
15068
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5178
South Asian (SAS)
AF:
AC:
0
AN:
4830
European-Finnish (FIN)
AF:
AC:
0
AN:
10546
Middle Eastern (MID)
AF:
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67926
Other (OTH)
AF:
AC:
1
AN:
2084
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.542
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.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Conflicting classifications of pathogenicity
Revision:criteria provided, conflicting classifications
Pathogenic
VUS
Benign
Condition
-
1
1
not provided (2)
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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