rs4284050

Variant names:

• chr8-69628633-A-C
• rs4284050
• NM_001128205.2:c.2108+397A>C

Your query was ambiguous. Multiple possible variants found:

• chr8-69628633-A-C
• chr8-69628633-A-G
• chr8-69628633-A-T

Variant summary

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

The NM_001128205.2(SULF1):​c.2108+397A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 152,046 control chromosomes in the GnomAD database, including 27,416 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 0.60 (27416 hom., cov: 33)
• Consequence: SULF1 NM_001128205.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULF1	NM_001128205.2	c.2108+397A>C		intron_variant	Intron 18 of 22	ENST00000402687.9	NP_001121677.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULF1	ENST00000402687.9	c.2108+397A>C		intron_variant	Intron 18 of 22	1	NM_001128205.2	ENSP00000385704.4

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90727 AN: 151928 Hom.: 27404 Cov.: 33

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.597 AC: 90789 AN: 152046 Hom.: 27416 Cov.: 33 AF XY: 0.597 AC XY: 44390 AN XY: 74296

African (AFR) AF: 0.619 AC: 25669 AN: 41442

American (AMR) AF: 0.658 AC: 10056 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2015 AN: 3470

East Asian (EAS) AF: 0.667 AC: 3457 AN: 5184

South Asian (SAS) AF: 0.483 AC: 2325 AN: 4812

European-Finnish (FIN) AF: 0.592 AC: 6251 AN: 10556

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39069 AN: 67978

Other (OTH) AF: 0.593 AC: 1249 AN: 2106

Alfa AF: 0.580 Hom.: 31848

Bravo AF: 0.607

Asia WGS AF: 0.575 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.70
DANN	Benign	0.38
PhyloP100		-0.29
Mutation Taster		=100/0	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: rs4284050; hg19: chr8-70540868;