rs551820424
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_014905.5(GLS):c.1039-5dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000325 in 1,475,334 control chromosomes in the GnomAD database, including 2 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_014905.5 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00146 AC: 222AN: 151694Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000496 AC: 123AN: 248216Hom.: 1 AF XY: 0.000372 AC XY: 50AN XY: 134298
GnomAD4 exome AF: 0.000196 AC: 259AN: 1323520Hom.: 2 Cov.: 21 AF XY: 0.000165 AC XY: 110AN XY: 666062
GnomAD4 genome AF: 0.00146 AC: 221AN: 151814Hom.: 0 Cov.: 32 AF XY: 0.00156 AC XY: 116AN XY: 74192
ClinVar
Submissions by phenotype
GLS-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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at