10-97767816-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_003015.3(SFRP5):c.652C>T(p.Arg218Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00107 in 1,538,538 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0058 ( 6 hom., cov: 32)
Exomes 𝑓: 0.00056 ( 8 hom. )
Consequence
SFRP5
NM_003015.3 missense
NM_003015.3 missense
Scores
2
8
8
Clinical Significance
Conservation
PhyloP100: 2.82
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 made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.008385897).
BP6
?
Variant 10-97767816-G-A is Benign according to our data. Variant chr10-97767816-G-A is described in ClinVar as [Benign]. Clinvar id is 717162.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00579 (881/152172) while in subpopulation AFR AF= 0.0201 (834/41514). AF 95% confidence interval is 0.019. There are 6 homozygotes in gnomad4. There are 387 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 6 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SFRP5 | NM_003015.3 | c.652C>T | p.Arg218Trp | missense_variant | 3/3 | ENST00000266066.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFRP5 | ENST00000266066.4 | c.652C>T | p.Arg218Trp | missense_variant | 3/3 | 1 | NM_003015.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00579 AC: 880AN: 152054Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.00174 AC: 320AN: 183546Hom.: 3 AF XY: 0.00127 AC XY: 123AN XY: 96894
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GnomAD4 exome AF: 0.000556 AC: 771AN: 1386366Hom.: 8 Cov.: 31 AF XY: 0.000511 AC XY: 349AN XY: 682732
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GnomAD4 genome ? AF: 0.00579 AC: 881AN: 152172Hom.: 6 Cov.: 32 AF XY: 0.00520 AC XY: 387AN XY: 74396
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 29, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at