12-65056267-CTTTT-CTT
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_007191.5(WIF1):c.827-143_827-142delAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000253 in 485,230 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000085 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00033 ( 0 hom. )
Consequence
WIF1
NM_007191.5 intron
NM_007191.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.28
Genes affected
WIF1 (HGNC:18081): (WNT inhibitory factor 1) The protein encoded by this gene functions to inhibit WNT proteins, which are extracellular signaling molecules that play a role in embryonic development. This protein contains a WNT inhibitory factor (WIF) domain and five epidermal growth factor (EGF)-like domains, and is thought to be involved in mesoderm segmentation. This gene functions as a tumor suppressor gene, and has been found to be epigenetically silenced in various cancers. [provided by RefSeq, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000847 AC: 1AN: 118004Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.000332 AC: 122AN: 367226Hom.: 0 AF XY: 0.000321 AC XY: 61AN XY: 190254
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GnomAD4 genome AF: 0.00000847 AC: 1AN: 118004Hom.: 0 Cov.: 31 AF XY: 0.0000178 AC XY: 1AN XY: 56134
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ClinVar
Not reported inComputational scores
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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