dbSNP rs765476443: KDM1A:p.Ala12_Ala14del (chr1-23019623-CGCGGCGGCG-C) – ACMG Classification: Uncertain_significance (1 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP3

The NM_001009999.3(KDM1A):c.33_41delGGCGGCGGC(p.Ala12_Ala14del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000316 in 1,266,376 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000032 ( 0 hom. )

Consequence

KDM1A
NM_001009999.3 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.82

Publications

0 publications found

Variant links:

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 syndrome
Inheritance: AD Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Orphanet

KDM1A links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP3

Nonframeshift variant in repetitive region in NM_001009999.3

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

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
KDM1A	NM_001009999.3	MANE Select	c.33_41delGGCGGCGGC	p.Ala12_Ala14del	disruptive_inframe_deletion	Exon 1 of 21	NP_001009999.1	O60341-2
KDM1A	NM_001410762.1		c.33_41delGGCGGCGGC	p.Ala12_Ala14del	disruptive_inframe_deletion	Exon 1 of 20	NP_001397691.1	A0A8I5KXU4
KDM1A	NM_001363654.2		c.33_41delGGCGGCGGC	p.Ala12_Ala14del	disruptive_inframe_deletion	Exon 1 of 19	NP_001350583.1	R4GMQ1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
KDM1A	ENST00000400181.9	TSL:1 MANE Select	c.33_41delGGCGGCGGC	p.Ala12_Ala14del	disruptive_inframe_deletion	Exon 1 of 21	ENSP00000383042.5	O60341-2
KDM1A	ENST00000356634.7	TSL:1	c.33_41delGGCGGCGGC	p.Ala12_Ala14del	disruptive_inframe_deletion	Exon 1 of 19	ENSP00000349049.3	O60341-1
KDM1A	ENST00000874661.1		c.33_41delGGCGGCGGC	p.Ala12_Ala14del	disruptive_inframe_deletion	Exon 1 of 21	ENSP00000544720.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000316

AC:

AN:

1266376

Hom.:

AF XY:

0.00

AC XY:

AN XY:

623036

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

25464

American (AMR)

AF:

0.00

AC:

AN:

17278

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19726

East Asian (EAS)

AF:

0.00

AC:

AN:

29544

South Asian (SAS)

AF:

0.00

AC:

AN:

60458

European-Finnish (FIN)

AF:

0.00

AC:

AN:

31272

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3552

European-Non Finnish (NFE)

AF:

0.00000389

AC:

AN:

1027244

Other (OTH)

AF:

0.00

AC:

AN:

51838

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over