22-45923322-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_058238.3(WNT7B):c.584G>A(p.Arg195Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000492 in 1,605,554 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R195W) has been classified as Uncertain significance.
Frequency
Consequence
NM_058238.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WNT7B | ENST00000339464.9 | c.584G>A | p.Arg195Gln | missense_variant | Exon 4 of 4 | 1 | NM_058238.3 | ENSP00000341032.4 | ||
WNT7B | ENST00000409496.7 | c.596G>A | p.Arg199Gln | missense_variant | Exon 4 of 4 | 2 | ENSP00000386546.3 | |||
WNT7B | ENST00000410089.5 | c.536G>A | p.Arg179Gln | missense_variant | Exon 4 of 4 | 5 | ENSP00000386781.1 |
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152230Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000690 AC: 17AN: 246244Hom.: 0 AF XY: 0.0000676 AC XY: 9AN XY: 133230
GnomAD4 exome AF: 0.0000358 AC: 52AN: 1453324Hom.: 0 Cov.: 32 AF XY: 0.0000305 AC XY: 22AN XY: 721642
GnomAD4 genome AF: 0.000177 AC: 27AN: 152230Hom.: 0 Cov.: 34 AF XY: 0.000161 AC XY: 12AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.584G>A (p.R195Q) alteration is located in exon 4 (coding exon 4) of the WNT7B gene. This alteration results from a G to A substitution at nucleotide position 584, causing the arginine (R) at amino acid position 195 to be replaced by a glutamine (Q). 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