10-100482273-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_003393.4(WNT8B):c.513G>A(p.Ala171=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00452 in 1,582,078 control chromosomes in the GnomAD database, including 168 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_003393.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WNT8B | NM_003393.4 | c.513G>A | p.Ala171= | splice_region_variant, synonymous_variant | 6/6 | ENST00000343737.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNT8B | ENST00000343737.6 | c.513G>A | p.Ala171= | splice_region_variant, synonymous_variant | 6/6 | 1 | NM_003393.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0186 AC: 2824AN: 152202Hom.: 79 Cov.: 32
GnomAD3 exomes AF: 0.00671 AC: 1507AN: 224722Hom.: 30 AF XY: 0.00603 AC XY: 742AN XY: 123066
GnomAD4 exome AF: 0.00302 AC: 4320AN: 1429758Hom.: 89 Cov.: 33 AF XY: 0.00308 AC XY: 2184AN XY: 709034
GnomAD4 genome AF: 0.0186 AC: 2831AN: 152320Hom.: 79 Cov.: 32 AF XY: 0.0181 AC XY: 1350AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 13, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at