rs200470034
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_003179.3(SYP):āc.5T>Gā(p.Leu2Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000571 in 1,051,091 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L2Q) has been classified as Likely benign.
Frequency
Consequence
NM_003179.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYP | NM_003179.3 | c.5T>G | p.Leu2Arg | missense_variant | 1/7 | ENST00000263233.9 | |
SYP-AS1 | NR_046649.1 | n.386+958A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYP | ENST00000263233.9 | c.5T>G | p.Leu2Arg | missense_variant | 1/7 | 1 | NM_003179.3 | P1 | |
SYP-AS1 | ENST00000433499.1 | n.259+958A>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 exomes AF: 0.00000963 AC: 1AN: 103834Hom.: 0 AF XY: 0.0000287 AC XY: 1AN XY: 34798
GnomAD4 exome AF: 0.00000571 AC: 6AN: 1051091Hom.: 0 Cov.: 30 AF XY: 0.0000117 AC XY: 4AN XY: 342891
GnomAD4 genome ? Cov.: 23
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at