rs149245953
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM2
The NM_025216.3(WNT10A):c.667C>A(p.Arg223Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,610,964 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R223C) has been classified as Uncertain significance.
Frequency
Consequence
NM_025216.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WNT10A | NM_025216.3 | c.667C>A | p.Arg223Ser | missense_variant | 3/4 | ENST00000258411.8 | |
WNT10A | XM_011511929.3 | c.571C>A | p.Arg191Ser | missense_variant | 4/5 | ||
WNT10A | XM_011511930.2 | c.377-2500C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNT10A | ENST00000258411.8 | c.667C>A | p.Arg223Ser | missense_variant | 3/4 | 1 | NM_025216.3 | P1 | |
WNT10A | ENST00000458582.1 | c.264-2500C>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152152Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000203 AC: 5AN: 245718Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 133678
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1458694Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 725846
GnomAD4 genome AF: 0.000151 AC: 23AN: 152270Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74456
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at