rs281865036
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_ModeratePM2PP5
The NM_024312.5(GNPTAB):c.3434+1G>A variant causes a splice donor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000747 in 1,338,590 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_024312.5 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GNPTAB | NM_024312.5 | c.3434+1G>A | splice_donor_variant, intron_variant | Intron 18 of 20 | ENST00000299314.12 | NP_077288.2 | ||
GNPTAB | XM_011538731.3 | c.3353+1G>A | splice_donor_variant, intron_variant | Intron 18 of 20 | XP_011537033.1 | |||
GNPTAB | XM_006719593.4 | c.3434+1G>A | splice_donor_variant, intron_variant | Intron 18 of 18 | XP_006719656.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GNPTAB | ENST00000299314.12 | c.3434+1G>A | splice_donor_variant, intron_variant | Intron 18 of 20 | 1 | NM_024312.5 | ENSP00000299314.7 | |||
GNPTAB | ENST00000550718.1 | c.245+1G>A | splice_donor_variant, intron_variant | Intron 3 of 3 | 3 | ENSP00000449557.1 | ||||
GNPTAB | ENST00000549194.1 | n.301G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 3 | |||||
GNPTAB | ENST00000549738.5 | n.185+1G>A | splice_donor_variant, intron_variant | Intron 2 of 4 | 4 | ENSP00000450161.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 7.47e-7 AC: 1AN: 1338590Hom.: 0 Cov.: 21 AF XY: 0.00000149 AC XY: 1AN XY: 672404
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Mucolipidosis type II Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at