rs6990375
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_001128205.2(SULF1):c.*761G>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 0.301 in 423,916 control chromosomes in the GnomAD database, including 19,992 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 0.31 ( 7455 hom., cov: 32)
Exomes 𝑓: 0.30 ( 12537 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: 3.48
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SULF1 | NM_001128205.2 | c.*761G>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.*761G>A | 3_prime_UTR_variant | 23/23 | 1 | NM_001128205.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.308 AC: 46787AN: 151896Hom.: 7458 Cov.: 32
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GnomAD3 exomes AF: 0.321 AC: 35361AN: 110102Hom.: 5877 AF XY: 0.312 AC XY: 18205AN XY: 58356
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GnomAD4 exome AF: 0.297 AC: 80745AN: 271904Hom.: 12537 Cov.: 0 AF XY: 0.286 AC XY: 44285AN XY: 154738
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GnomAD4 genome ? AF: 0.308 AC: 46807AN: 152012Hom.: 7455 Cov.: 32 AF XY: 0.311 AC XY: 23085AN XY: 74286
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at