chr17-46875094-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_003396.3(WNT9B):c.335-7G>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000298 in 1,613,386 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003396.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WNT9B | NM_003396.3 | c.335-7G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000290015.7 | |||
WNT9B | NM_001320458.2 | c.335-7G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
WNT9B | XM_011525178.3 | c.353-7G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
LRRC37A2 | XM_024450773.2 | c.4810-173962G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNT9B | ENST00000290015.7 | c.335-7G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003396.3 | P1 | |||
WNT9B | ENST00000393461.2 | c.335-7G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
WNT9B | ENST00000575372.5 | c.353-7G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152102Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 247362Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134464
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461284Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 726968
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152102Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74294
ClinVar
Submissions by phenotype
WNT9B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 19, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at