rs3793975
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000263321.6(TYR):c.1184+50G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 1,596,530 control chromosomes in the GnomAD database, including 14,655 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.17 ( 2607 hom., cov: 32)
Exomes 𝑓: 0.12 ( 12048 hom. )
Consequence
TYR
ENST00000263321.6 intron
ENST00000263321.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.107
Genes affected
TYR (HGNC:12442): (tyrosinase) The enzyme encoded by this gene catalyzes the first 2 steps, and at least 1 subsequent step, in the conversion of tyrosine to melanin. The enzyme has both tyrosine hydroxylase and dopa oxidase catalytic activities, and requires copper for function. Mutations in this gene result in oculocutaneous albinism, and nonpathologic polymorphisms result in skin pigmentation variation. The human genome contains a pseudogene similar to the 3' half of this gene. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
Variant 11-89228020-G-A is Benign according to our data. Variant chr11-89228020-G-A is described in ClinVar as [Benign]. Clinvar id is 1281825.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TYR | NM_000372.5 | c.1184+50G>A | intron_variant | ENST00000263321.6 | NP_000363.1 | |||
TYR | XM_011542970.3 | c.1184+50G>A | intron_variant | XP_011541272.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TYR | ENST00000263321.6 | c.1184+50G>A | intron_variant | 1 | NM_000372.5 | ENSP00000263321 | P1 |
Frequencies
GnomAD3 genomes AF: 0.167 AC: 25355AN: 151862Hom.: 2587 Cov.: 32
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GnomAD3 exomes AF: 0.140 AC: 34747AN: 248150Hom.: 2897 AF XY: 0.140 AC XY: 18844AN XY: 134410
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GnomAD4 exome AF: 0.122 AC: 176056AN: 1444552Hom.: 12048 Cov.: 27 AF XY: 0.124 AC XY: 89574AN XY: 719698
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GnomAD4 genome AF: 0.167 AC: 25421AN: 151978Hom.: 2607 Cov.: 32 AF XY: 0.168 AC XY: 12483AN XY: 74234
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 15, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at