chr9-6981115-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_015061.6(KDM4C):c.1112G>A(p.Arg371Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00318 in 1,610,256 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_015061.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KDM4C | NM_015061.6 | c.1112G>A | p.Arg371Gln | missense_variant | 9/22 | ENST00000381309.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KDM4C | ENST00000381309.8 | c.1112G>A | p.Arg371Gln | missense_variant | 9/22 | 1 | NM_015061.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00261 AC: 397AN: 152134Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00231 AC: 571AN: 246654Hom.: 2 AF XY: 0.00229 AC XY: 306AN XY: 133408
GnomAD4 exome AF: 0.00324 AC: 4729AN: 1458004Hom.: 13 Cov.: 31 AF XY: 0.00304 AC XY: 2206AN XY: 725230
GnomAD4 genome ? AF: 0.00261 AC: 397AN: 152252Hom.: 2 Cov.: 32 AF XY: 0.00238 AC XY: 177AN XY: 74452
ClinVar
Submissions by phenotype
Maffucci syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Baylor-Hopkins Center for Mendelian Genomics, Johns Hopkins University School of Medicine | - | - - |
KDM4C-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 15, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at