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4-153781713-T-C

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP3BP6_ModerateBS2

The NM_003013.3(SFRP2):c.626A>G(p.Asp209Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 1,614,176 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000079 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00013 ( 0 hom. )

Consequence

SFRP2
NM_003013.3 missense

Scores

3
10
6

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 7.23
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PP3
MetaRNN computational evidence supports a deleterious effect, 0.763
BP6
Variant 4-153781713-T-C is Benign according to our data. Variant chr4-153781713-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 221956.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd at 12 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SFRP2NM_003013.3 linkuse as main transcriptc.626A>G p.Asp209Gly missense_variant 3/3 ENST00000274063.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SFRP2ENST00000274063.5 linkuse as main transcriptc.626A>G p.Asp209Gly missense_variant 3/31 NM_003013.3 P1

Frequencies

GnomAD3 genomes
AF:
0.0000788
AC:
12
AN:
152196
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000724
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000132
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000318
AC:
8
AN:
251442
Hom.:
0
AF XY:
0.0000221
AC XY:
3
AN XY:
135898
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000703
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000126
AC:
184
AN:
1461862
Hom.:
0
Cov.:
31
AF XY:
0.000117
AC XY:
85
AN XY:
727234
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000159
Gnomad4 OTH exome
AF:
0.0000993
GnomAD4 genome
AF:
0.0000788
AC:
12
AN:
152314
Hom.:
0
Cov.:
32
AF XY:
0.0000805
AC XY:
6
AN XY:
74488
show subpopulations
Gnomad4 AFR
AF:
0.0000722
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000132
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000132
Hom.:
0
Bravo
AF:
0.0000680
ExAC
AF:
0.00000824
AC:
1

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Anophthalmia-microphthalmia syndrome Benign:1
Likely benign, criteria provided, single submitterclinical testingPaul Sabatier University EA-4555, Paul Sabatier UniversityJan 01, 2013- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.70
BayesDel_addAF
Uncertain
0.085
D
BayesDel_noAF
Uncertain
0.070
Cadd
Uncertain
24
Dann
Uncertain
1.0
DEOGEN2
Benign
0.33
T
Eigen
Uncertain
0.34
Eigen_PC
Uncertain
0.45
FATHMM_MKL
Uncertain
0.85
D
LIST_S2
Uncertain
0.93
D
M_CAP
Benign
0.030
D
MetaRNN
Pathogenic
0.76
D
MetaSVM
Benign
-0.97
T
MutationAssessor
Uncertain
2.0
M
MutationTaster
Benign
1.0
D
PrimateAI
Uncertain
0.78
T
PROVEAN
Pathogenic
-4.8
D
REVEL
Uncertain
0.46
Sift
Benign
0.071
T
Sift4G
Benign
0.065
T
Polyphen
0.20
B
Vest4
0.87
MVP
0.68
MPC
1.3
ClinPred
0.28
T
GERP RS
5.8
Varity_R
0.62
gMVP
0.87

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.

Other links and lift over

dbSNP: rs770485715; hg19: chr4-154702865; API