chr3-13818812-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004625.4(WNT7A):c.*132C>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 0.00122 in 1,369,774 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0062 ( 9 hom., cov: 32)
Exomes 𝑓: 0.00060 ( 3 hom. )
Consequence
WNT7A
NM_004625.4 3_prime_UTR
NM_004625.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.515
Genes affected
WNT7A (HGNC:12786): (Wnt family member 7A) This gene is a member of the WNT gene family, which 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 involved in the development of the anterior-posterior axis in the female reproductive tract, and also plays a critical role in uterine smooth muscle pattering and maintenance of adult uterine function. Mutations in this gene are associated with Fuhrmann and Al-Awadi/Raas-Rothschild/Schinzel phocomelia syndromes. [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 (BayesDel_noAF=-0.89).
BP6
?
Variant 3-13818812-G-A is Benign according to our data. Variant chr3-13818812-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1212528.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00619 (942/152102) while in subpopulation AFR AF= 0.0212 (880/41460). AF 95% confidence interval is 0.0201. There are 9 homozygotes in gnomad4. There are 453 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WNT7A | NM_004625.4 | c.*132C>T | 3_prime_UTR_variant | 4/4 | ENST00000285018.5 | ||
WNT7A | XM_011534091.3 | c.*132C>T | 3_prime_UTR_variant | 5/5 | |||
WNT7A | XM_047448863.1 | c.*132C>T | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNT7A | ENST00000285018.5 | c.*132C>T | 3_prime_UTR_variant | 4/4 | 1 | NM_004625.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00620 AC: 942AN: 151986Hom.: 9 Cov.: 32
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GnomAD4 exome AF: 0.000600 AC: 730AN: 1217672Hom.: 3 Cov.: 19 AF XY: 0.000541 AC XY: 320AN XY: 591594
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GnomAD4 genome ? AF: 0.00619 AC: 942AN: 152102Hom.: 9 Cov.: 32 AF XY: 0.00609 AC XY: 453AN XY: 74354
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 23, 2020 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at