rs200462975
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_000360.4(TH):c.313-38_313-35del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00914 in 968,646 control chromosomes in the GnomAD database, including 362 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.010 ( 41 hom., cov: 30)
Exomes 𝑓: 0.0089 ( 321 hom. )
Consequence
TH
NM_000360.4 intron
NM_000360.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0720
Genes affected
TH (HGNC:11782): (tyrosine hydroxylase) The protein encoded by this gene is involved in the conversion of tyrosine to dopamine. It is the rate-limiting enzyme in the synthesis of catecholamines, hence plays a key role in the physiology of adrenergic neurons. Mutations in this gene have been associated with autosomal recessive Segawa syndrome. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 11-2168699-GAGAA-G is Benign according to our data. Variant chr11-2168699-GAGAA-G is described in ClinVar as [Likely_benign]. Clinvar id is 263255.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0555 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TH | NM_000360.4 | c.313-38_313-35del | intron_variant | ENST00000352909.8 | |||
TH | NM_199292.3 | c.406-38_406-35del | intron_variant | ||||
TH | NM_199293.3 | c.394-38_394-35del | intron_variant | ||||
TH | XM_011520335.3 | c.325-38_325-35del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TH | ENST00000352909.8 | c.313-38_313-35del | intron_variant | 1 | NM_000360.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0104 AC: 1383AN: 133082Hom.: 41 Cov.: 30
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GnomAD3 exomes AF: 0.0220 AC: 4504AN: 204318Hom.: 250 AF XY: 0.0173 AC XY: 1946AN XY: 112634
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GnomAD4 exome AF: 0.00893 AC: 7464AN: 835474Hom.: 321 AF XY: 0.00776 AC XY: 3314AN XY: 426974
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GnomAD4 genome ? AF: 0.0104 AC: 1387AN: 133172Hom.: 41 Cov.: 30 AF XY: 0.0126 AC XY: 797AN XY: 63152
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2019 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at