chr3-13819370-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_004625.4(WNT7A):c.624G>A(p.Ser208=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000312 in 1,613,260 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0017 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00017 ( 2 hom. )
Consequence
WNT7A
NM_004625.4 synonymous
NM_004625.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.10
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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
Variant 3-13819370-C-T is Benign according to our data. Variant chr3-13819370-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 743183.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-1.1 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00169 (258/152278) while in subpopulation AFR AF= 0.00604 (251/41546). AF 95% confidence interval is 0.00543. There are 3 homozygotes in gnomad4. There are 118 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WNT7A | NM_004625.4 | c.624G>A | p.Ser208= | synonymous_variant | 4/4 | ENST00000285018.5 | |
WNT7A | XM_011534091.3 | c.423G>A | p.Ser141= | synonymous_variant | 5/5 | ||
WNT7A | XM_047448863.1 | c.423G>A | p.Ser141= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNT7A | ENST00000285018.5 | c.624G>A | p.Ser208= | synonymous_variant | 4/4 | 1 | NM_004625.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00170 AC: 258AN: 152160Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.000392 AC: 98AN: 250286Hom.: 0 AF XY: 0.000185 AC XY: 25AN XY: 135208
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GnomAD4 exome AF: 0.000168 AC: 245AN: 1460982Hom.: 2 Cov.: 31 AF XY: 0.000131 AC XY: 95AN XY: 726756
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 28, 2022 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 11, 2021 | - - |
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