dbSNP rs13238899: SUMF2:c.225-72T>G (chr7-56072925-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015411.4(SUMF2):c.225-72T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0759 in 1,127,292 control chromosomes in the GnomAD database, including 4,346 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 0.083 ( 623 hom., cov: 32)

Exomes 𝑓: 0.075 ( 3723 hom. )

Consequence

SUMF2
NM_015411.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.605

Publications

17 publications found

Variant links:

Genes affected

SUMF2 (HGNC:20415): (sulfatase modifying factor 2) The catalytic sites of sulfatases are only active if they contain a unique amino acid, C-alpha-formylglycine (FGly). The FGly residue is posttranslationally generated from a cysteine by enzymes with FGly-generating activity. The gene described in this record is a member of the sulfatase-modifying factor family and encodes a protein with a DUF323 domain that localizes to the lumen of the endoplasmic reticulum. This protein has low levels of FGly-generating activity but can heterodimerize with another family member - a protein with high levels of FGly-generating activity. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

SUMF2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUMF2	NM_015411.4 link	c.225-72T>G		intron_variant	Intron 2 of 8	ENST00000434526.8	NP_056226.3	Q8NBJ7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUMF2	ENST00000434526.8 link	c.225-72T>G		intron_variant	Intron 2 of 8	1	NM_015411.4	ENSP00000400922.3		Q8NBJ7-1

Frequencies

GnomAD3 genomes

AF:

0.0826

AC:

12564

AN:

152096

Hom.:

622

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0852

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.105

Gnomad ASJ

AF:

0.0548

Gnomad EAS

AF:

0.235

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.111

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0599

Gnomad OTH

AF:

0.0817

GnomAD4 exome

AF:

0.0748

AC:

72970

AN:

975078

Hom.:

3723

AF XY:

0.0755

AC XY:

37705

AN XY:

499534

show subpopulations

African (AFR)

AF:

0.0920

AC:

2195

AN:

23866

American (AMR)

AF:

0.146

AC:

5844

AN:

40030

Ashkenazi Jewish (ASJ)

AF:

0.0569

AC:

1153

AN:

20254

East Asian (EAS)

AF:

0.251

AC:

9339

AN:

37266

South Asian (SAS)

AF:

0.110

AC:

7602

AN:

69044

European-Finnish (FIN)

AF:

0.102

AC:

5222

AN:

51154

Middle Eastern (MID)

AF:

0.0625

AC:

293

AN:

4690

European-Non Finnish (NFE)

AF:

0.0557

AC:

38166

AN:

684652

Other (OTH)

AF:

0.0715

AC:

3156

AN:

44122

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

3475

6950

10426

13901

17376

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1334

2668

4002

5336

6670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0826

AC:

12579

AN:

152214

Hom.:

623

Cov.:

AF XY:

0.0882

AC XY:

6566

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.0855

AC:

3553

AN:

41556

American (AMR)

AF:

0.105

AC:

1603

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.0548

AC:

190

AN:

3468

East Asian (EAS)

AF:

0.235

AC:

1210

AN:

5158

South Asian (SAS)

AF:

0.118

AC:

567

AN:

4822

European-Finnish (FIN)

AF:

0.111

AC:

1172

AN:

10602

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0599

AC:

4071

AN:

68018

Other (OTH)

AF:

0.0814

AC:

172

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

587

1174

1762

2349

2936

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

150

300

450

600

750

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0706

Hom.:

1454

Bravo

AF:

0.0827

Asia WGS

AF:

0.154

AC:

532

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

5.5

(source)

DANN

Benign

0.88

PhyloP100

0.60

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over