2-86456416-A-ATTT
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_018433.6(KDM3A):c.557-6_557-4dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.00020 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0061 ( 1 hom. )
Consequence
KDM3A
NM_018433.6 intron
NM_018433.6 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.593
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP6
Variant 2-86456416-A-ATTT is Benign according to our data. Variant chr2-86456416-A-ATTT is described in ClinVar as [Benign]. Clinvar id is 3049186.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High AC in GnomAd4 at 25 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KDM3A | NM_018433.6 | c.557-6_557-4dup | intron_variant | ENST00000312912.10 | NP_060903.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KDM3A | ENST00000312912.10 | c.557-6_557-4dup | intron_variant | 1 | NM_018433.6 | ENSP00000323659 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000201 AC: 25AN: 124184Hom.: 0 Cov.: 0
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GnomAD3 exomes AF: 0.0176 AC: 547AN: 31146Hom.: 2 AF XY: 0.0182 AC XY: 315AN XY: 17322
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GnomAD4 exome AF: 0.00606 AC: 5625AN: 927632Hom.: 1 Cov.: 0 AF XY: 0.00630 AC XY: 2894AN XY: 459132
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GnomAD4 genome AF: 0.000201 AC: 25AN: 124168Hom.: 0 Cov.: 0 AF XY: 0.000172 AC XY: 10AN XY: 58218
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
KDM3A-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 25, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at