Variant rs2281279 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001387048.1(SULF2):c.2494+267A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 298,968 control chromosomes in the GnomAD database, including 10,444 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 0.25 ( 5058 hom., cov: 31)

Exomes 𝑓: 0.26 ( 5386 hom. )

Consequence

SULF2
NM_001387048.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.794

Variant links:

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]

SULF2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SULF2	NM_001387048.1 linkuse as main transcript	c.2494+267A>G		intron_variant		ENST00000688720.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SULF2	ENST00000688720.1 linkuse as main transcript	c.2494+267A>G		intron_variant			NM_001387048.1	P3	Q8IWU5-1

Frequencies

GnomAD3 genomes

AF:

0.253

AC:

38414

AN:

151970

Hom.:

5058

Cov.:

show subpopulations

Gnomad AFR

AF:

0.197

Gnomad AMI

AF:

0.471

Gnomad AMR

AF:

0.248

Gnomad ASJ

AF:

0.326

Gnomad EAS

AF:

0.180

Gnomad SAS

AF:

0.252

Gnomad FIN

AF:

0.189

Gnomad MID

AF:

0.364

Gnomad NFE

AF:

0.296

Gnomad OTH

AF:

0.274

GnomAD4 exome

AF:

0.263

AC:

38588

AN:

146880

Hom.:

5386

Cov.:

AF XY:

0.264

AC XY:

19438

AN XY:

73612

show subpopulations

Gnomad4 AFR exome

AF:

0.202

Gnomad4 AMR exome

AF:

0.225

Gnomad4 ASJ exome

AF:

0.321

Gnomad4 EAS exome

AF:

0.162

Gnomad4 SAS exome

AF:

0.261

Gnomad4 FIN exome

AF:

0.199

Gnomad4 NFE exome

AF:

0.293

Gnomad4 OTH exome

AF:

0.281

GnomAD4 genome

AF:

0.253

AC:

38424

AN:

152088

Hom.:

5058

Cov.:

AF XY:

0.247

AC XY:

18353

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.197

Gnomad4 AMR

AF:

0.248

Gnomad4 ASJ

AF:

0.326

Gnomad4 EAS

AF:

0.180

Gnomad4 SAS

AF:

0.251

Gnomad4 FIN

AF:

0.189

Gnomad4 NFE

AF:

0.296

Gnomad4 OTH

AF:

0.276

Alfa

AF:

0.294

Hom.:

7742

Bravo

AF:

0.255

Asia WGS

AF:

0.234

AC:

820

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

4.9

DANN

Benign

0.80

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over