rs12725747
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003395.4(WNT9A):c.*2298C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,240 control chromosomes in the GnomAD database, including 866 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 0.10 ( 866 hom., cov: 32)
Exomes 𝑓: 0.036 ( 0 hom. )
Consequence
WNT9A
NM_003395.4 3_prime_UTR
NM_003395.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.882
Genes affected
WNT9A (HGNC:12778): (Wnt family member 9A) The WNT gene family consists of structurally related genes that encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene is a member of the WNT gene family. It is expressed in gastric cancer cell lines. The protein encoded by this gene shows 75% amino acid identity to chicken Wnt14, which has been shown to play a central role in initiating synovial joint formation in the chick limb. This gene is clustered with another family member, WNT3A, in the chromosome 1q42 region. [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=-0.85).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WNT9A | NM_003395.4 | c.*2298C>T | 3_prime_UTR_variant | 4/4 | ENST00000272164.6 | ||
WNT9A | XM_011544271.3 | c.*2298C>T | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNT9A | ENST00000272164.6 | c.*2298C>T | 3_prime_UTR_variant | 4/4 | 1 | NM_003395.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.101 AC: 15377AN: 152094Hom.: 865 Cov.: 32
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GnomAD4 exome AF: 0.0357 AC: 1AN: 28Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 20
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GnomAD4 genome ? AF: 0.101 AC: 15371AN: 152212Hom.: 866 Cov.: 32 AF XY: 0.102 AC XY: 7565AN XY: 74420
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ClinVar
Not reported inComputational 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