rs13273088

Positions:

• chr8-69581739-G-A
• chr8-69581739-G-C
• chr8-69581739-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001128205.2(SULF1):​c.413-4618G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,124 control chromosomes in the GnomAD database, including 49,525 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 0.80 (49525 hom., cov: 32)
• Consequence: SULF1 NM_001128205.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SULF1	NM_001128205.2	c.413-4618G>A		intron_variant		ENST00000402687.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SULF1	ENST00000402687.9	c.413-4618G>A		intron_variant		1	NM_001128205.2	P1

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122318 AN: 152006 Hom.: 49476 Cov.: 32

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.795

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.805 AC: 122421 AN: 152124 Hom.: 49525 Cov.: 32 AF XY: 0.803 AC XY: 59721 AN XY: 74346

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.839

Gnomad4 EAS AF: 0.830

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.800

Gnomad4 OTH AF: 0.797

Alfa AF: 0.799 Hom.: 26485

Bravo AF: 0.796

Asia WGS AF: 0.809 AC: 2815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	16
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs13273088; hg19: chr8-70493974;