rs12839420
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001320752.2(STS):c.-186G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000989 in 1,010,816 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. 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_001320752.2 5_prime_UTR
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 |
---|---|---|---|---|---|---|---|
STS | NM_001320752.2 | c.-186G>A | 5_prime_UTR_variant | 1/11 | ENST00000674429.1 | ||
PUDP | NM_012080.5 | c.61+22C>T | intron_variant | ENST00000381077.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STS | ENST00000674429.1 | c.-186G>A | 5_prime_UTR_variant | 1/11 | NM_001320752.2 | P1 | |||
PUDP | ENST00000381077.10 | c.61+22C>T | intron_variant | 1 | NM_012080.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD4 exome AF: 9.89e-7 AC: 1AN: 1010816Hom.: 0 Cov.: 24 AF XY: 0.00000314 AC XY: 1AN XY: 318846
GnomAD4 genome ? Cov.: 23
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at