1-23019614-GGCGGCAGCCGCGGCGGCGGCGGCTGCA-G

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The ENST00000400181.9(KDM1A):​c.27_53del​(p.Ala10_Ala18del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000365 in 1,426,404 control chromosomes in the GnomAD database, including 4 homozygotes. Variant has been reported in ClinVar as Benign (β˜…). Synonymous variant affecting the same amino acid position (i.e. A7A) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.00081 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00031 ( 3 hom. )

Consequence

KDM1A
ENST00000400181.9 inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.52
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6
Variant 1-23019614-GGCGGCAGCCGCGGCGGCGGCGGCTGCA-G is Benign according to our data. Variant chr1-23019614-GGCGGCAGCCGCGGCGGCGGCGGCTGCA-G is described in ClinVar as [Benign]. Clinvar id is 1970962.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 124 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KDM1ANM_001009999.3 linkuse as main transcriptc.27_53del p.Ala10_Ala18del inframe_deletion 1/21 ENST00000400181.9 NP_001009999.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KDM1AENST00000400181.9 linkuse as main transcriptc.27_53del p.Ala10_Ala18del inframe_deletion 1/211 NM_001009999.3 ENSP00000383042 O60341-2

Frequencies

GnomAD3 genomes
AF:
0.000809
AC:
123
AN:
152090
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000217
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00622
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0000944
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000177
Gnomad OTH
AF:
0.00287
GnomAD3 exomes
AF:
0.00105
AC:
76
AN:
72596
Hom.:
2
AF XY:
0.000733
AC XY:
31
AN XY:
42298
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00738
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000137
Gnomad OTH exome
AF:
0.00198
GnomAD4 exome
AF:
0.000311
AC:
396
AN:
1274206
Hom.:
3
AF XY:
0.000303
AC XY:
190
AN XY:
627324
show subpopulations
Gnomad4 AFR exome
AF:
0.000195
Gnomad4 AMR exome
AF:
0.00855
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000492
Gnomad4 FIN exome
AF:
0.0000318
Gnomad4 NFE exome
AF:
0.000195
Gnomad4 OTH exome
AF:
0.000479
GnomAD4 genome
AF:
0.000815
AC:
124
AN:
152198
Hom.:
1
Cov.:
32
AF XY:
0.000806
AC XY:
60
AN XY:
74416
show subpopulations
Gnomad4 AFR
AF:
0.000217
Gnomad4 AMR
AF:
0.00628
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0000944
Gnomad4 NFE
AF:
0.000177
Gnomad4 OTH
AF:
0.00284
Alfa
AF:
0.000712
Hom.:
0
Bravo
AF:
0.00139
Asia WGS
AF:
0.000290
AC:
1
AN:
3460

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 22, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs762119456; hg19: chr1-23346107; API