rs3093542
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000595.4(LTA):c.100-12G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,894 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000595.4 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LTA | NM_000595.4 | c.100-12G>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000418386.3 | |||
LTA | NM_001159740.2 | c.100-12G>A | splice_polypyrimidine_tract_variant, intron_variant | ||||
LTA | XM_047418773.1 | c.100-12G>A | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LTA | ENST00000418386.3 | c.100-12G>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000595.4 | P1 | |||
LTA | ENST00000454783.5 | c.100-12G>A | splice_polypyrimidine_tract_variant, intron_variant | 2 | P1 | ||||
LTA | ENST00000471842.1 | n.336G>A | non_coding_transcript_exon_variant | 2/3 | 2 | ||||
LTA | ENST00000489638.5 | n.216G>A | non_coding_transcript_exon_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 29
GnomAD3 exomes AF: 0.00000406 AC: 1AN: 246190Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134194
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459894Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1AN XY: 726322
GnomAD4 genome ? Cov.: 29
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at