rs765476443

Variant names:

• chr1-23019623-CGCG-C
• rs765476443
• NM_001009999.3:c.39_41delGGC

Your query was ambiguous. Multiple possible variants found:

• chr1-23019623-CGCG-C
• chr1-23019623-CGCG-CGCGGCG

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001009999.3(KDM1A):​c.39_41delGGC​(p.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 0.00054 in 1,261,444 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A13A) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00054 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: KDM1A NM_001009999.3 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.77

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 681 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KDM1A	NM_001009999.3	c.39_41delGGC	p.Ala14del	disruptive_inframe_deletion	Exon 1 of 21	ENST00000400181.9	NP_001009999.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KDM1A	ENST00000400181.9	c.39_41delGGC	p.Ala14del	disruptive_inframe_deletion	Exon 1 of 21	1	NM_001009999.3	ENSP00000383042.5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 151708 Hom.: 0 Cov.: 32 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00324 AC: 190 AN: 58636 Hom.: 0 AF XY: 0.00348 AC XY: 120 AN XY: 34436

Gnomad AFR exome AF: 0.00120

Gnomad AMR exome AF: 0.00389

Gnomad ASJ exome AF: 0.00428

Gnomad EAS exome AF: 0.000334

Gnomad SAS exome AF: 0.00516

Gnomad FIN exome AF: 0.00192

Gnomad NFE exome AF: 0.00284

Gnomad OTH exome AF: 0.00633

GnomAD4 exome AF: 0.000540 AC: 681 AN: 1261444 Hom.: 0 AF XY: 0.000668 AC XY: 414 AN XY: 620174

Gnomad4 AFR exome AF: 0.000157

Gnomad4 AMR exome AF: 0.00233

Gnomad4 ASJ exome AF: 0.00128

Gnomad4 EAS exome AF: 0.000102

Gnomad4 SAS exome AF: 0.00266

Gnomad4 FIN exome AF: 0.000869

Gnomad4 NFE exome AF: 0.000372

Gnomad4 OTH exome AF: 0.000736

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 151708 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 74084

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs765476443; hg19: chr1-23346116;