rs80338775
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_ModeratePM2PP3_Moderate
The NM_080669.6(SLC46A1):c.1082-1G>C variant causes a splice acceptor change. The variant allele was found at a frequency of 0.00000657 in 152,220 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 1/1 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_080669.6 splice_acceptor
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC46A1 | NM_080669.6 | c.1082-1G>C | splice_acceptor_variant | ENST00000612814.5 | |||
SARM1 | NM_015077.4 | c.*6036C>G | 3_prime_UTR_variant | 9/9 | ENST00000585482.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC46A1 | ENST00000612814.5 | c.1082-1G>C | splice_acceptor_variant | 2 | NM_080669.6 | P1 | |||
SARM1 | ENST00000585482.6 | c.*6036C>G | 3_prime_UTR_variant | 9/9 | 1 | NM_015077.4 | P1 | ||
SLC46A1 | ENST00000618626.1 | c.1082-1556G>C | intron_variant | 1 | |||||
SLC46A1 | ENST00000582735.1 | c.206+2294G>C | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 33
GnomAD4 exome Cov.: 30
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74362
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at