chr2-86456416-ATT-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_018433.6(KDM3A):c.557-5_557-4delTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0135 in 1,044,710 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_018433.6 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000805 AC: 10AN: 124186Hom.: 0 Cov.: 0
GnomAD3 exomes AF: 0.0266 AC: 827AN: 31146Hom.: 0 AF XY: 0.0285 AC XY: 494AN XY: 17322
GnomAD4 exome AF: 0.0154 AC: 14132AN: 920540Hom.: 0 AF XY: 0.0159 AC XY: 7218AN XY: 455286
GnomAD4 genome AF: 0.0000805 AC: 10AN: 124170Hom.: 0 Cov.: 0 AF XY: 0.0000687 AC XY: 4AN XY: 58212
ClinVar
Submissions by phenotype
KDM3A-related disorder Benign:1
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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at