NM_003015.3:c.527C>T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2PP3
The NM_003015.3(SFRP5):c.527C>T(p.Pro176Leu) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SFRP5
NM_003015.3 missense, splice_region
NM_003015.3 missense, splice_region
Scores
1
9
8
Splicing: ADA: 0.9990
2
Clinical Significance
Conservation
PhyloP100: 9.67
Publications
0 publications found
Genes affected
SFRP5 (HGNC:10779): (secreted frizzled related protein 5) Secreted frizzled-related protein 5 (SFRP5) is 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. SFRP5 and SFRP1 may be involved in determining the polarity of photoreceptor cells in the retina. SFRP5 is highly expressed in the retinal pigment epithelium, and moderately expressed in the pancreas. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. Scorers claiming Benign: max_spliceai.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_003015.3. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00000558 AC: 1AN: 179066 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
179066
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1413318Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 698798
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1413318
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
698798
African (AFR)
AF:
AC:
0
AN:
31796
American (AMR)
AF:
AC:
0
AN:
37182
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24346
East Asian (EAS)
AF:
AC:
0
AN:
37474
South Asian (SAS)
AF:
AC:
0
AN:
81112
European-Finnish (FIN)
AF:
AC:
0
AN:
49240
Middle Eastern (MID)
AF:
AC:
0
AN:
5244
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1088708
Other (OTH)
AF:
AC:
0
AN:
58216
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Uncertain
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Benign
D
Sift4G
Uncertain
T
Polyphen
B
Vest4
MutPred
Loss of glycosylation at T173 (P = 0.0419)
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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