NM_018433.6:c.557-14_557-4delTTTTTTTTTTT

Variant names:

• chr2-86456416-ATTTTTTTTTTT-A
• rs11431031
• NM_018433.6:c.557-14_557-4delTTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_018433.6(KDM3A):​c.557-14_557-4delTTTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000321 in 933,664 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0000032 (0 hom.)
• Consequence: KDM3A NM_018433.6 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.12
• Publications: 0 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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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.557-14_557-4delTTTTTTTTTTT		splice_region intron	N/A	NP_060903.2
	KDM3A	NM_001146688.2		c.557-14_557-4delTTTTTTTTTTT		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.557-25_557-15delTTTTTTTTTTT		intron	N/A	ENSP00000323659.5	Q9Y4C1
	KDM3A	ENST00000409064.5	TSL:1	c.557-25_557-15delTTTTTTTTTTT		intron	N/A	ENSP00000386516.1	Q9Y4C1
	KDM3A	ENST00000900202.1		c.557-25_557-15delTTTTTTTTTTT		intron	N/A	ENSP00000570261.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000321 AC: 3 AN: 933664 Hom.: 0 AF XY: 0.00000433 AC XY: 2 AN XY: 462170

African (AFR) AF: 0.00 AC: 0 AN: 18308

American (AMR) AF: 0.00 AC: 0 AN: 11292

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15228

East Asian (EAS) AF: 0.00 AC: 0 AN: 24038

South Asian (SAS) AF: 0.00 AC: 0 AN: 43448

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 35878

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2664

European-Non Finnish (NFE) AF: 0.00000403 AC: 3 AN: 744332

Other (OTH) AF: 0.00 AC: 0 AN: 38476

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs11431031; hg19: chr2-86683539;