rs3087714
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001128205.2(SULF1):c.*2234G>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 0.299 in 152,348 control chromosomes in the GnomAD database, including 7,136 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 0.30 ( 7108 hom., cov: 33)
Exomes 𝑓: 0.34 ( 28 hom. )
Consequence
SULF1
NM_001128205.2 3_prime_UTR
NM_001128205.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.757
Genes affected
SULF1 (HGNC:20391): (sulfatase 1) This gene encodes an extracellular heparan sulfate endosulfatase. The encoded enzyme selectively removes 6-O-sulfate groups from heparan sulfate chains of heparan sulfate proteoglycans (HSPGs). The enzyme is secreted through the Golgi and is subsequently localized to the cell surface. The expression of this gene may be down-regulated in several types of cancer, including hepatocellular (HCC), ovarian and breast cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
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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=-0.49).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SULF1 | NM_001128205.2 | c.*2234G>A | 3_prime_UTR_variant | 23/23 | ENST00000402687.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SULF1 | ENST00000402687.9 | c.*2234G>A | 3_prime_UTR_variant | 23/23 | 1 | NM_001128205.2 | P1 | ||
SULF1 | ENST00000458141.6 | c.*2234G>A | 3_prime_UTR_variant | 22/22 | 1 | P1 | |||
SULF1 | ENST00000260128.8 | c.*2234G>A | 3_prime_UTR_variant | 23/23 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.299 AC: 45399AN: 151798Hom.: 7110 Cov.: 33
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GnomAD4 exome AF: 0.345 AC: 149AN: 432Hom.: 28 Cov.: 0 AF XY: 0.327 AC XY: 85AN XY: 260
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GnomAD4 genome ? AF: 0.299 AC: 45419AN: 151916Hom.: 7108 Cov.: 33 AF XY: 0.302 AC XY: 22445AN XY: 74240
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ClinVar
Not reported inComputational scores
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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