NM_001128225.3:c.-9+3G>T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001128225.3(SLC39A13):c.-9+3G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001128225.3 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 2144Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 1452
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
The c.-30+3 G>T variant of uncertain significance in the SLC39A13 gene has not been published as pathogenic or been reported as benign to our knowledge. This variant is located in intron 1 of the 5' untranslated region of the SLC39A13 gene, which is the non-coding region upstream of the start codon located in exon 2. Specifically, this variant occurs in the natural splice donor site of intron 1, at a nucleotide that is conserved in mammals. However, in silico splice algorithms predict that this variant likely does not alter splicing. Additionally, no other regulatory or splice site variants in the SLC39A13 gene have been reported in HGMD in association with spEDS to date (Stenson et al., 2014). Nevertheless, in the absence of functional mRNA studies, the physiological consequence of this variant cannot be precisely determined. Furthermore, data from control individuals was not available to assess whether c.-30+3 G>T may be a common benign variant in the general population.Therefore, based on the currently available information, it is unclear whether this variant is pathogenic or rare benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at