20-47658268-C-G

Variant names:

• chr20-47658268-C-G
• rs444271
• NM_001387048.1:c.*94G>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.*94G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.897 in 1,384,818 control chromosomes in the GnomAD database, including 557,361 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 0.92 (64981 hom., cov: 33)
  • Exomes 𝑓: 0.89 (492380 hom.)
• Consequence: SULF2 NM_001387048.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.483
• Publications: 11 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULF2	NM_001387048.1	c.*94G>C		3_prime_UTR_variant	Exon 21 of 21	ENST00000688720.1	NP_001373977.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULF2	ENST00000688720.1	c.*94G>C		3_prime_UTR_variant	Exon 21 of 21		NM_001387048.1	ENSP00000508753.1

Frequencies

GnomAD3 genomes AF: 0.923 AC: 140434 AN: 152176 Hom.: 64922 Cov.: 33

Gnomad AFR AF: 0.977

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.930

GnomAD4 exome AF: 0.893 AC: 1101048 AN: 1232524 Hom.: 492380 Cov.: 17 AF XY: 0.894 AC XY: 558612 AN XY: 624684

African (AFR) AF: 0.981 AC: 28417 AN: 28954

American (AMR) AF: 0.891 AC: 39339 AN: 44164

Ashkenazi Jewish (ASJ) AF: 0.936 AC: 23181 AN: 24778

East Asian (EAS) AF: 0.974 AC: 37645 AN: 38666

South Asian (SAS) AF: 0.913 AC: 74560 AN: 81654

European-Finnish (FIN) AF: 0.907 AC: 48287 AN: 53228

Middle Eastern (MID) AF: 0.965 AC: 5151 AN: 5340

European-Non Finnish (NFE) AF: 0.882 AC: 796777 AN: 902948

Other (OTH) AF: 0.903 AC: 47691 AN: 52792

GnomAD4 genome AF: 0.923 AC: 140551 AN: 152294 Hom.: 64981 Cov.: 33 AF XY: 0.927 AC XY: 69038 AN XY: 74448

African (AFR) AF: 0.977 AC: 40628 AN: 41568

American (AMR) AF: 0.928 AC: 14193 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3229 AN: 3472

East Asian (EAS) AF: 0.964 AC: 4995 AN: 5184

South Asian (SAS) AF: 0.907 AC: 4377 AN: 4826

European-Finnish (FIN) AF: 0.914 AC: 9695 AN: 10604

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.887 AC: 60315 AN: 68022

Other (OTH) AF: 0.931 AC: 1968 AN: 2114

Alfa AF: 0.902 Hom.: 7737

Bravo AF: 0.928

Asia WGS AF: 0.923 AC: 3209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.41
PhyloP100		0.48
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: rs444271; hg19: chr20-46287012;