chr20-967264-A-G
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_001029871.4(RSPO4):c.319T>C(p.Cys107Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,614,084 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C107Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_001029871.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RSPO4 | NM_001029871.4 | c.319T>C | p.Cys107Arg | missense_variant | 3/5 | ENST00000217260.9 | |
RSPO4 | NM_001040007.3 | c.319T>C | p.Cys107Arg | missense_variant | 3/4 | ||
RSPO4 | XM_017027839.2 | c.319T>C | p.Cys107Arg | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RSPO4 | ENST00000217260.9 | c.319T>C | p.Cys107Arg | missense_variant | 3/5 | 1 | NM_001029871.4 | P1 | |
RSPO4 | ENST00000400634.2 | c.319T>C | p.Cys107Arg | missense_variant | 3/4 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249546Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135392
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461852Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 727230
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74372
ClinVar
Submissions by phenotype
Anonychia Pathogenic:2
Pathogenic, no assertion criteria provided | clinical testing | Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare | - | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 2006 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at