chrX-30653624-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBS2_Supporting
The NM_001205019.2(GK):c.78+9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000143 in 1,194,119 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 57 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001205019.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000107 AC: 12AN: 112335Hom.: 0 Cov.: 24 AF XY: 0.000145 AC XY: 5AN XY: 34497
GnomAD3 exomes AF: 0.000104 AC: 19AN: 182782Hom.: 0 AF XY: 0.0000888 AC XY: 6AN XY: 67604
GnomAD4 exome AF: 0.000147 AC: 159AN: 1081784Hom.: 0 Cov.: 28 AF XY: 0.000149 AC XY: 52AN XY: 348096
GnomAD4 genome AF: 0.000107 AC: 12AN: 112335Hom.: 0 Cov.: 24 AF XY: 0.000145 AC XY: 5AN XY: 34497
ClinVar
Submissions by phenotype
GK-related disorder Benign:1
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). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at