rs1927598075
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_ModeratePM2PP5_Moderate
The NM_000330.4(RS1):c.649delC(p.Leu217TrpfsTer20) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_000330.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RS1 | NM_000330.4 | c.649delC | p.Leu217TrpfsTer20 | frameshift_variant | Exon 6 of 6 | ENST00000379984.4 | NP_000321.1 | |
RS1 | XM_047442337.1 | c.553delC | p.Leu185TrpfsTer20 | frameshift_variant | Exon 4 of 4 | XP_047298293.1 | ||
CDKL5 | NM_001037343.2 | c.2714-3977delG | intron_variant | Intron 19 of 21 | NP_001032420.1 | |||
CDKL5 | NM_003159.3 | c.2714-3977delG | intron_variant | Intron 18 of 20 | NP_003150.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RS1 | ENST00000379984.4 | c.649delC | p.Leu217TrpfsTer20 | frameshift_variant | Exon 6 of 6 | 1 | NM_000330.4 | ENSP00000369320.3 | ||
CDKL5 | ENST00000379989.6 | c.2714-3977delG | intron_variant | Intron 19 of 21 | 1 | ENSP00000369325.3 | ||||
CDKL5 | ENST00000379996.7 | c.2714-3977delG | intron_variant | Intron 18 of 20 | 1 | ENSP00000369332.3 | ||||
RS1 | ENST00000476595.1 | n.1140delC | non_coding_transcript_exon_variant | Exon 5 of 5 | 1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
Juvenile retinoschisis Pathogenic:1
This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PM2. This variant was detected in hemizygous state. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at