rs1889177

Variant names:

• chr20-47682774-G-A
• rs1889177
• NM_001387048.1:c.1064+220C>T

Variant summary

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

The NM_001387048.1(SULF2):​c.1064+220C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,010 control chromosomes in the GnomAD database, including 19,149 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 0.50 (19149 hom., cov: 32)
• Consequence: SULF2 NM_001387048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.32
• Publications: 6 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]

ENSG00000255438 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULF2	NM_001387048.1	MANE Select	c.1064+220C>T		intron	N/A	NP_001373977.1
	SULF2	NM_001387052.1		c.1064+220C>T		intron	N/A	NP_001373981.1
	SULF2	NM_001387053.1		c.1064+220C>T		intron	N/A	NP_001373982.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULF2	ENST00000688720.1	MANE Select	c.1064+220C>T		intron	N/A	ENSP00000508753.1
	SULF2	ENST00000359930.8	TSL:1	c.1064+220C>T		intron	N/A	ENSP00000353007.4
	SULF2	ENST00000484875.5	TSL:1	c.1064+220C>T		intron	N/A	ENSP00000418290.1

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75419 AN: 151894 Hom.: 19131 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.497 AC: 75486 AN: 152010 Hom.: 19149 Cov.: 32 AF XY: 0.504 AC XY: 37449 AN XY: 74316

African (AFR) AF: 0.477 AC: 19760 AN: 41448

American (AMR) AF: 0.485 AC: 7409 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1080 AN: 3470

East Asian (EAS) AF: 0.650 AC: 3351 AN: 5158

South Asian (SAS) AF: 0.575 AC: 2775 AN: 4822

European-Finnish (FIN) AF: 0.636 AC: 6736 AN: 10586

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33016 AN: 67928

Other (OTH) AF: 0.473 AC: 998 AN: 2110

Alfa AF: 0.476 Hom.: 29467

Bravo AF: 0.482

Asia WGS AF: 0.608 AC: 2110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.11
DANN	Benign	0.67
PhyloP100		-3.3
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: rs1889177; hg19: chr20-46311518; COSMIC: COSV63420720; COSMIC: COSV63420720;