rs3760091
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001055.4(SULT1A1):c.-5+452G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 1,141,004 control chromosomes in the GnomAD database, including 80,245 homozygotes. 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
Genomes: 𝑓 0.38 ( 9428 hom., cov: 37)
Exomes 𝑓: 0.40 ( 70817 hom. )
Consequence
SULT1A1
NM_001055.4 intron
NM_001055.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.48
Genes affected
SULT1A1 (HGNC:11453): (sulfotransferase family 1A member 1) Sulfotransferase enzymes catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs, and xenobiotic compounds. These cytosolic enzymes are different in their tissue distributions and substrate specificities. The gene structure (number and length of exons) is similar among family members. This gene encodes one of two phenol sulfotransferases with thermostable enzyme activity. Multiple alternatively spliced variants that encode two isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.09).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SULT1A1 | NM_001055.4 | c.-5+452G>C | intron_variant | ENST00000314752.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SULT1A1 | ENST00000314752.12 | c.-5+452G>C | intron_variant | 1 | NM_001055.4 | P1 | |||
SULT1A1 | ENST00000566189.5 | c.-36+452G>C | intron_variant | 5 | |||||
SULT1A1 | ENST00000567512.1 | c.-5+452G>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.380 AC: 57251AN: 150576Hom.: 9420 Cov.: 37
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GnomAD3 exomes AF: 0.378 AC: 48484AN: 128248Hom.: 8168 AF XY: 0.376 AC XY: 26261AN XY: 69790
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GnomAD4 exome AF: 0.397 AC: 393604AN: 990310Hom.: 70817 Cov.: 15 AF XY: 0.394 AC XY: 193413AN XY: 490840
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GnomAD4 genome ? AF: 0.380 AC: 57290AN: 150694Hom.: 9428 Cov.: 37 AF XY: 0.380 AC XY: 28000AN XY: 73588
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ClinVar
Not reported inComputational scores
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Name
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Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at