dbSNP rs4076441: SFRP2:p.Phe26Phe (chr4-153788758-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_003013.3(SFRP2):c.78C>T(p.Phe26Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0131 in 1,612,152 control chromosomes in the GnomAD database, including 518 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 0.037 ( 240 hom., cov: 32)

Exomes 𝑓: 0.011 ( 278 hom. )

Consequence

SFRP2
NM_003013.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.21

Publications

4 publications found

Variant links:

Genes affected

SFRP2 (HGNC:10777): (secreted frizzled related protein 2) This gene encodes a member of the SFRP family that contains a cysteine-rich domain homologous to the putative Wnt-binding site of Frizzled proteins. SFRPs act as soluble modulators of Wnt signaling. Methylation of this gene is a potential marker for the presence of colorectal cancer. [provided by RefSeq, Jul 2008]

SFRP2 links:

ENSG00000280241 (HGNC:):

ENSG00000280241 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP7

Synonymous conserved (PhyloP=1.21 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFRP2	NM_003013.3 link	c.78C>T	p.Phe26Phe	synonymous_variant	Exon 1 of 3	ENST00000274063.5	NP_003004.1	Q96HF1A0A140VJU3B3KSM5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFRP2	ENST00000274063.5 link	c.78C>T	p.Phe26Phe	synonymous_variant	Exon 1 of 3	1	NM_003013.3	ENSP00000274063.4		Q96HF1

Frequencies

GnomAD3 genomes

AF:

0.0371

AC:

5639

AN:

152186

Hom.:

240

Cov.:

show subpopulations

Gnomad AFR

AF:

0.104

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0296

Gnomad ASJ

AF:

0.0384

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.00724

Gnomad FIN

AF:

0.00104

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.00826

Gnomad OTH

AF:

0.0530

GnomAD2 exomes

AF:

0.0170

AC:

4161

AN:

245324

AF XY:

0.0155

show subpopulations

Gnomad AFR exome

AF:

0.109

Gnomad AMR exome

AF:

0.0205

Gnomad ASJ exome

AF:

0.0437

Gnomad EAS exome

AF:

0.000110

Gnomad FIN exome

AF:

0.00116

Gnomad NFE exome

AF:

0.00879

Gnomad OTH exome

AF:

0.0230

GnomAD4 exome

AF:

0.0107

AC:

15548

AN:

1459848

Hom.:

278

Cov.:

AF XY:

0.0106

AC XY:

7686

AN XY:

726274

show subpopulations

African (AFR)

AF:

0.107

AC:

3568

AN:

33474

American (AMR)

AF:

0.0220

AC:

986

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.0408

AC:

1067

AN:

26130

East Asian (EAS)

AF:

0.0000504

AC:

AN:

39698

South Asian (SAS)

AF:

0.00808

AC:

697

AN:

86252

European-Finnish (FIN)

AF:

0.00124

AC:

AN:

51538

Middle Eastern (MID)

AF:

0.0695

AC:

397

AN:

5714

European-Non Finnish (NFE)

AF:

0.00677

AC:

7525

AN:

1111958

Other (OTH)

AF:

0.0206

AC:

1242

AN:

60364

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

969

1937

2906

3874

4843

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

354

708

1062

1416

1770

<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:

0.0370

AC:

5639

AN:

152304

Hom.:

240

Cov.:

AF XY:

0.0367

AC XY:

2731

AN XY:

74472

show subpopulations

African (AFR)

AF:

0.104

AC:

4304

AN:

41550

American (AMR)

AF:

0.0295

AC:

451

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.0384

AC:

133

AN:

3468

East Asian (EAS)

AF:

0.000387

AC:

AN:

5166

South Asian (SAS)

AF:

0.00745

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.00104

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00825

AC:

561

AN:

68034

Other (OTH)

AF:

0.0515

AC:

109

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

268

535

803

1070

1338

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

174

232

290

<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:

0.0203

Hom.:

Bravo

AF:

0.0428

Asia WGS

AF:

0.0100

AC:

AN:

3478

EpiCase

AF:

0.0124

EpiControl

AF:

0.0132

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

9.2

(source)

DANN

Benign

0.72

PhyloP100

1.2

PromoterAI

-0.043

Neutral

(source)

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