rs4788068
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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.*419G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 284,640 control chromosomes in the GnomAD database, including 15,804 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 0.34 ( 8979 hom., cov: 35)
Exomes 𝑓: 0.33 ( 6825 hom. )
Consequence
SULT1A1
NM_001055.4 3_prime_UTR
NM_001055.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.45
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=-0.94).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SULT1A1 | NM_001055.4 | c.*419G>A | 3_prime_UTR_variant | 8/8 | ENST00000314752.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SULT1A1 | ENST00000314752.12 | c.*419G>A | 3_prime_UTR_variant | 8/8 | 1 | NM_001055.4 | P1 | ||
SULT1A1 | ENST00000569554.5 | c.*419G>A | 3_prime_UTR_variant | 7/7 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.341 AC: 51083AN: 149974Hom.: 8970 Cov.: 35
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GnomAD4 exome AF: 0.329 AC: 44208AN: 134556Hom.: 6825 Cov.: 0 AF XY: 0.315 AC XY: 23187AN XY: 73572
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GnomAD4 genome ? AF: 0.341 AC: 51132AN: 150084Hom.: 8979 Cov.: 35 AF XY: 0.342 AC XY: 25047AN XY: 73254
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at