12-48966366-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_003394.4(WNT10B):c.899G>A(p.Arg300His) variant causes a missense change. The variant allele was found at a frequency of 0.0000304 in 1,614,070 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003394.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WNT10B | ENST00000301061.9 | c.899G>A | p.Arg300His | missense_variant | Exon 5 of 5 | 1 | NM_003394.4 | ENSP00000301061.4 | ||
WNT10B | ENST00000407467 | c.*181G>A | 3_prime_UTR_variant | Exon 6 of 6 | 2 | ENSP00000384691.1 | ||||
WNT10B | ENST00000403957 | c.*181G>A | 3_prime_UTR_variant | Exon 6 of 6 | 5 | ENSP00000385980.1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250698Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135700
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461876Hom.: 0 Cov.: 34 AF XY: 0.0000234 AC XY: 17AN XY: 727242
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74338
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.899G>A (p.R300H) alteration is located in exon 5 (coding exon 4) of the WNT10B gene. This alteration results from a G to A substitution at nucleotide position 899, causing the arginine (R) at amino acid position 300 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at