rs13264163

Variant names:

• chr8-69501925-A-G
• rs13264163
• NM_001128205.2:c.-177A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001128205.2(SULF1):​c.-177A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,256 control chromosomes in the GnomAD database, including 2,896 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 0.17 (2896 hom., cov: 32)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: SULF1 NM_001128205.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULF1	NM_001128205.2	c.-177A>G		5_prime_UTR_variant	Exon 3 of 23	ENST00000402687.9	NP_001121677.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULF1	ENST00000402687.9	c.-177A>G		5_prime_UTR_variant	Exon 3 of 23	1	NM_001128205.2	ENSP00000385704.4

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26241 AN: 152128 Hom.: 2893 Cov.: 32

Gnomad AFR AF: 0.0386

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.192

GnomAD4 exome AF: 0.100 AC: 1 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 6

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.172 AC: 26251 AN: 152246 Hom.: 2896 Cov.: 32 AF XY: 0.177 AC XY: 13205 AN XY: 74422

African (AFR) AF: 0.0385 AC: 1601 AN: 41574

American (AMR) AF: 0.167 AC: 2561 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3472

East Asian (EAS) AF: 0.167 AC: 865 AN: 5178

South Asian (SAS) AF: 0.316 AC: 1522 AN: 4822

European-Finnish (FIN) AF: 0.281 AC: 2974 AN: 10588

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.224 AC: 15231 AN: 68002

Other (OTH) AF: 0.197 AC: 417 AN: 2112

Alfa AF: 0.201 Hom.: 8123

Bravo AF: 0.156

Asia WGS AF: 0.205 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	16
DANN	Benign	0.85
PhyloP100		1.3
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13264163; hg19: chr8-70414160;