1-43703696-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014663.3(KDM4A):āc.2921G>Cā(p.Gly974Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,862 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. G974G) has been classified as Likely benign.
Frequency
Consequence
NM_014663.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KDM4A | NM_014663.3 | c.2921G>C | p.Gly974Ala | missense_variant | 20/22 | ENST00000372396.4 | NP_055478.2 | |
KDM4A-AS1 | NR_033827.1 | n.389-49C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KDM4A | ENST00000372396.4 | c.2921G>C | p.Gly974Ala | missense_variant | 20/22 | 1 | NM_014663.3 | ENSP00000361473.3 | ||
ENSG00000284989 | ENST00000645057.1 | n.*1159G>C | non_coding_transcript_exon_variant | 14/26 | ENSP00000494063.1 | |||||
ENSG00000284989 | ENST00000645057.1 | n.*1159G>C | 3_prime_UTR_variant | 14/26 | ENSP00000494063.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251486Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135918
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461862Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727228
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 14, 2024 | The c.2921G>C (p.G974A) alteration is located in exon 20 (coding exon 19) of the KDM4A gene. This alteration results from a G to C substitution at nucleotide position 2921, causing the glycine (G) at amino acid position 974 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at