rs2762464
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000550.3(TYRP1):c.*404A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 184,574 control chromosomes in the GnomAD database, including 25,646 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.46 ( 20460 hom., cov: 32)
Exomes 𝑓: 0.51 ( 5186 hom. )
Consequence
TYRP1
NM_000550.3 3_prime_UTR
NM_000550.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.623
Genes affected
TYRP1 (HGNC:12450): (tyrosinase related protein 1) This gene encodes a melanosomal enzyme that belongs to the tyrosinase family and plays an important role in the melanin biosynthetic pathway. Defects in this gene are the cause of rufous oculocutaneous albinism and oculocutaneous albinism type III. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 9-12709586-A-T is Benign according to our data. Variant chr9-12709586-A-T is described in ClinVar as [Benign]. Clinvar id is 364865.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TYRP1 | NM_000550.3 | c.*404A>T | 3_prime_UTR_variant | 8/8 | ENST00000388918.10 | ||
LURAP1L-AS1 | NR_125775.1 | n.317-8960T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TYRP1 | ENST00000388918.10 | c.*404A>T | 3_prime_UTR_variant | 8/8 | 1 | NM_000550.3 | P1 | ||
LURAP1L-AS1 | ENST00000417638.1 | n.273-8960T>A | intron_variant, non_coding_transcript_variant | 3 | |||||
LURAP1L-AS1 | ENST00000650458.1 | n.193-10231T>A | intron_variant, non_coding_transcript_variant | ||||||
LURAP1L-AS1 | ENST00000654076.1 | n.159-8960T>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.459 AC: 69687AN: 151660Hom.: 20460 Cov.: 32
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GnomAD4 exome AF: 0.508 AC: 16657AN: 32798Hom.: 5186 Cov.: 0 AF XY: 0.483 AC XY: 8307AN XY: 17208
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GnomAD4 genome ? AF: 0.459 AC: 69686AN: 151776Hom.: 20460 Cov.: 32 AF XY: 0.453 AC XY: 33573AN XY: 74184
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
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. - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at