rs4810671

Variant names:

• chr20-47726848-A-G
• rs4810671
• NM_001387048.1:c.415+9855T>C

Variant summary

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

The NM_001387048.1(SULF2):​c.415+9855T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 151,766 control chromosomes in the GnomAD database, including 5,371 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 0.26 (5371 hom., cov: 31)
• Consequence: SULF2 NM_001387048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.04
• Publications: 10 publications found

Genes affected

SULF2 (HGNC:20392): (sulfatase 2) Heparan sulfate proteoglycans (HSPGs) act as coreceptors for numerous heparin-binding growth factors and cytokines and are involved in cell signaling. Heparan sulfate 6-O-endosulfatases, such as SULF2, selectively remove 6-O-sulfate groups from heparan sulfate. This activity modulates the effects of heparan sulfate by altering binding sites for signaling molecules (Dai et al., 2005 [PubMed 16192265]).[supplied by OMIM, Mar 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001387048.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULF2	NM_001387048.1	MANE Select	c.415+9855T>C		intron	N/A	NP_001373977.1	Q8IWU5-1
	SULF2	NM_001387052.1		c.415+9855T>C		intron	N/A	NP_001373981.1
	SULF2	NM_001387053.1		c.415+9855T>C		intron	N/A	NP_001373982.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULF2	ENST00000688720.1	MANE Select	c.415+9855T>C		intron	N/A	ENSP00000508753.1	Q8IWU5-1
	SULF2	ENST00000359930.8	TSL:1	c.415+9855T>C		intron	N/A	ENSP00000353007.4	Q8IWU5-1
	SULF2	ENST00000484875.5	TSL:1	c.415+9855T>C		intron	N/A	ENSP00000418290.1	Q8IWU5-1

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39809 AN: 151648 Hom.: 5362 Cov.: 31

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.263 AC: 39853 AN: 151766 Hom.: 5371 Cov.: 31 AF XY: 0.266 AC XY: 19723 AN XY: 74136

African (AFR) AF: 0.235 AC: 9703 AN: 41356

American (AMR) AF: 0.241 AC: 3681 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 624 AN: 3462

East Asian (EAS) AF: 0.318 AC: 1633 AN: 5142

South Asian (SAS) AF: 0.325 AC: 1561 AN: 4798

European-Finnish (FIN) AF: 0.343 AC: 3606 AN: 10522

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.269 AC: 18288 AN: 67920

Other (OTH) AF: 0.223 AC: 471 AN: 2110

Alfa AF: 0.260 Hom.: 14905

Bravo AF: 0.252

Asia WGS AF: 0.297 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.045
DANN	Benign	0.22
PhyloP100		-3.0
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: rs4810671; hg19: chr20-46355592;