rs141933171
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP4_ModerateBP6_ModerateBS1
The NM_020708.5(SLC12A5):c.2680-3C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,612,432 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_020708.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC12A5 | NM_020708.5 | c.2680-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000243964.7 | |||
SLC12A5 | NM_001134771.2 | c.2749-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC12A5 | ENST00000243964.7 | c.2680-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_020708.5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000645 AC: 98AN: 152040Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000175 AC: 44AN: 250948Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135620
GnomAD4 exome AF: 0.0000562 AC: 82AN: 1460274Hom.: 0 Cov.: 31 AF XY: 0.0000495 AC XY: 36AN XY: 726548
GnomAD4 genome ? AF: 0.000644 AC: 98AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.000713 AC XY: 53AN XY: 74378
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 34 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at