7-37914238-C-T
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_003014.4(SFRP4):c.567G>A(p.Thr189Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 1,612,808 control chromosomes in the GnomAD database, including 151,674 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.45 ( 15387 hom., cov: 33)
Exomes 𝑓: 0.43 ( 136287 hom. )
Consequence
SFRP4
NM_003014.4 synonymous
NM_003014.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.97
Genes affected
SFRP4 (HGNC:10778): (secreted frizzled related protein 4) Secreted frizzled-related protein 4 (SFRP4) 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. The expression of SFRP4 in ventricular myocardium correlates with apoptosis related gene expression. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant 7-37914238-C-T is Benign according to our data. Variant chr7-37914238-C-T is described in ClinVar as [Benign]. Clinvar id is 1332948.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-4.97 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SFRP4 | ENST00000436072.7 | c.567G>A | p.Thr189Thr | synonymous_variant | 3/6 | 1 | NM_003014.4 | ENSP00000410715.2 | ||
ENSG00000290149 | ENST00000476620.1 | c.-37-34602C>T | intron_variant | 4 | ENSP00000425858.1 | |||||
SFRP4 | ENST00000447200.2 | c.165G>A | p.Thr55Thr | synonymous_variant | 4/6 | 5 | ENSP00000402262.2 |
Frequencies
GnomAD3 genomes AF: 0.445 AC: 67626AN: 151898Hom.: 15364 Cov.: 33
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GnomAD3 exomes AF: 0.460 AC: 115715AN: 251382Hom.: 27551 AF XY: 0.463 AC XY: 62859AN XY: 135868
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GnomAD4 exome AF: 0.428 AC: 625023AN: 1460792Hom.: 136287 Cov.: 37 AF XY: 0.432 AC XY: 313782AN XY: 726760
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GnomAD4 genome AF: 0.445 AC: 67686AN: 152016Hom.: 15387 Cov.: 33 AF XY: 0.451 AC XY: 33555AN XY: 74322
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Pyle metaphyseal dysplasia Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
SFRP4-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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