rs6094192
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_147197.2(WFDC11):c.-134+1021C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 151,918 control chromosomes in the GnomAD database, including 2,520 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.18 ( 2520 hom., cov: 32)
Consequence
WFDC11
NM_147197.2 intron
NM_147197.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.11
Genes affected
WFDC11 (HGNC:20478): (WAP four-disulfide core domain 11) This gene encodes a member of the WAP-type four-disulfide core (WFDC) domain family. The WFDC domain, or WAP signature motif, contains eight cysteines forming four disulfide bonds at the core of the protein, and functions as a protease inhibitor. Most WFDC gene members are localized to chromosome 20q12-q13 in two clusters: centromeric and telomeric. This gene belongs to the telomeric cluster. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WFDC11 | NM_147197.2 | c.-134+1021C>T | intron_variant | ENST00000324384.4 | |||
WFDC11 | XM_047440080.1 | c.-294+1021C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WFDC11 | ENST00000324384.4 | c.-134+1021C>T | intron_variant | 1 | NM_147197.2 | P1 | |||
WFDC11 | ENST00000356562.6 | c.-134+1025C>T | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.175 AC: 26600AN: 151800Hom.: 2515 Cov.: 32
GnomAD3 genomes
?
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26600
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.175 AC: 26634AN: 151918Hom.: 2520 Cov.: 32 AF XY: 0.173 AC XY: 12878AN XY: 74262
GnomAD4 genome
?
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26634
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151918
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32
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12878
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74262
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660
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at