rs34509359
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_000550.3(TYRP1):c.259C>A(p.Arg87=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0543 in 1,613,566 control chromosomes in the GnomAD database, including 2,702 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. R87R) has been classified as Likely benign.
Frequency
Consequence
NM_000550.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TYRP1 | NM_000550.3 | c.259C>A | p.Arg87= | synonymous_variant | 2/8 | ENST00000388918.10 | |
TYRP1 | XM_047423841.1 | c.259C>A | p.Arg87= | synonymous_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TYRP1 | ENST00000388918.10 | c.259C>A | p.Arg87= | synonymous_variant | 2/8 | 1 | NM_000550.3 | P1 | |
TYRP1 | ENST00000473763.1 | c.259C>A | p.Arg87= | synonymous_variant | 2/2 | 4 | |||
TYRP1 | ENST00000459790.1 | n.514C>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0430 AC: 6545AN: 152068Hom.: 188 Cov.: 32
GnomAD3 exomes AF: 0.0450 AC: 11227AN: 249496Hom.: 325 AF XY: 0.0449 AC XY: 6053AN XY: 134846
GnomAD4 exome AF: 0.0555 AC: 81055AN: 1461382Hom.: 2514 Cov.: 31 AF XY: 0.0542 AC XY: 39436AN XY: 726934
GnomAD4 genome AF: 0.0430 AC: 6544AN: 152184Hom.: 188 Cov.: 32 AF XY: 0.0432 AC XY: 3213AN XY: 74390
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Oculocutaneous albinism type 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at