12-101757311-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_ModeratePM2PP3_Strong
The NM_024312.5(GNPTAB):c.3336-1G>T variant causes a splice acceptor change. The variant allele was found at a frequency of 0.00000658 in 152,020 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_024312.5 splice_acceptor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNPTAB | NM_024312.5 | c.3336-1G>T | splice_acceptor_variant | ENST00000299314.12 | |||
GNPTAB | XM_006719593.4 | c.3336-1G>T | splice_acceptor_variant | ||||
GNPTAB | XM_011538731.3 | c.3255-1G>T | splice_acceptor_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNPTAB | ENST00000299314.12 | c.3336-1G>T | splice_acceptor_variant | 1 | NM_024312.5 | P1 | |||
GNPTAB | ENST00000550718.1 | c.148-1G>T | splice_acceptor_variant | 3 | |||||
GNPTAB | ENST00000549738.5 | c.87-1G>T | splice_acceptor_variant, NMD_transcript_variant | 4 | |||||
GNPTAB | ENST00000549194.1 | n.202-1G>T | splice_acceptor_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152020Hom.: 0 Cov.: 33
GnomAD4 exome Cov.: 23
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152020Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74238
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at