rs768138495
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_StrongPM2
The NM_001029871.4(RSPO4):c.98del(p.Gly33AlafsTer193) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,730 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001029871.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RSPO4 | NM_001029871.4 | c.98del | p.Gly33AlafsTer193 | frameshift_variant | 2/5 | ENST00000217260.9 | |
RSPO4 | NM_001040007.3 | c.98del | p.Gly33AlafsTer131 | frameshift_variant | 2/4 | ||
RSPO4 | XM_017027839.2 | c.98del | p.Gly33AlafsTer194 | frameshift_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RSPO4 | ENST00000217260.9 | c.98del | p.Gly33AlafsTer193 | frameshift_variant | 2/5 | 1 | NM_001029871.4 | P1 | |
RSPO4 | ENST00000400634.2 | c.98del | p.Gly33AlafsTer131 | frameshift_variant | 2/4 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461730Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727168
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.