3-134222543-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002958.4(RYK):c.233-4C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000164 in 1,580,590 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002958.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RYK | NM_002958.4 | c.233-4C>T | splice_region_variant, intron_variant | Intron 1 of 14 | ENST00000623711.4 | NP_002949.2 | ||
RYK | NM_001005861.3 | c.233-4C>T | splice_region_variant, intron_variant | Intron 1 of 14 | NP_001005861.1 | |||
RYK | XR_007095716.1 | n.438-4C>T | splice_region_variant, intron_variant | Intron 1 of 11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RYK | ENST00000623711.4 | c.233-4C>T | splice_region_variant, intron_variant | Intron 1 of 14 | 1 | NM_002958.4 | ENSP00000485095.1 | |||
RYK | ENST00000620660.4 | c.233-4C>T | splice_region_variant, intron_variant | Intron 1 of 14 | 1 | ENSP00000478721.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151830Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000509 AC: 11AN: 216076Hom.: 0 AF XY: 0.0000513 AC XY: 6AN XY: 116896
GnomAD4 exome AF: 0.0000168 AC: 24AN: 1428760Hom.: 0 Cov.: 28 AF XY: 0.0000155 AC XY: 11AN XY: 709810
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151830Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74160
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at