rs1554923218
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4BP6_Moderate
The NM_000360.4(TH):c.672C>T(p.Tyr224Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000708 in 1,412,066 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 7.1e-7 ( 0 hom. )
Consequence
TH
NM_000360.4 synonymous
NM_000360.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.87
Publications
0 publications found
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]
TH Gene-Disease associations (from GenCC):
- TH-deficient dopa-responsive dystoniaInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet
- tyrosine hydroxylase deficiencyInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen, Myriad Women’s Health
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (REVEL=0.188).
BP6
Variant 11-2167458-G-A is Benign according to our data. Variant chr11-2167458-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 1078157.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 7.08e-7 AC: 1AN: 1412066Hom.: 0 Cov.: 33 AF XY: 0.00000143 AC XY: 1AN XY: 697742 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1412066
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
697742
show subpopulations
African (AFR)
AF:
AC:
0
AN:
32502
American (AMR)
AF:
AC:
0
AN:
37576
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25264
East Asian (EAS)
AF:
AC:
0
AN:
37340
South Asian (SAS)
AF:
AC:
0
AN:
80198
European-Finnish (FIN)
AF:
AC:
0
AN:
48614
Middle Eastern (MID)
AF:
AC:
0
AN:
5708
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1086402
Other (OTH)
AF:
AC:
0
AN:
58462
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autosomal recessive DOPA responsive dystonia Benign:1
Aug 30, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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