rs17143305
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000361301.6(WNT16):c.*113C>T variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 963,024 control chromosomes in the GnomAD database, including 10,590 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000361301.6 splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WNT16 | ENST00000361301.6 | c.*113C>T | splice_region_variant | Exon 4 of 4 | 1 | ENSP00000355065.2 | ||||
WNT16 | ENST00000222462.3 | c.*113C>T | 3_prime_UTR_variant | Exon 4 of 4 | 1 | NM_057168.2 | ENSP00000222462.2 | |||
WNT16 | ENST00000361301.6 | c.*113C>T | 3_prime_UTR_variant | Exon 4 of 4 | 1 | ENSP00000355065.2 |
Frequencies
GnomAD3 genomes AF: 0.123 AC: 18010AN: 146492Hom.: 1341 Cov.: 32
GnomAD4 exome AF: 0.138 AC: 112921AN: 816428Hom.: 9248 Cov.: 11 AF XY: 0.136 AC XY: 56050AN XY: 410998
GnomAD4 genome AF: 0.123 AC: 18017AN: 146596Hom.: 1342 Cov.: 32 AF XY: 0.120 AC XY: 8606AN XY: 71618
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at