chr11-2164251-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000360.4(TH):c.1476G>T(p.Ala492=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000226 in 1,329,918 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 (★). Synonymous variant affecting the same amino acid position (i.e. A492A) has been classified as Likely benign.
Frequency
Consequence
NM_000360.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TH | NM_000360.4 | c.1476G>T | p.Ala492= | synonymous_variant | 13/13 | ENST00000352909.8 | |
TH | NM_199292.3 | c.1569G>T | p.Ala523= | synonymous_variant | 14/14 | ||
TH | NM_199293.3 | c.1557G>T | p.Ala519= | synonymous_variant | 14/14 | ||
TH | XM_011520335.3 | c.1488G>T | p.Ala496= | synonymous_variant | 13/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TH | ENST00000352909.8 | c.1476G>T | p.Ala492= | synonymous_variant | 13/13 | 1 | NM_000360.4 | P1 | |
TH | ENST00000381178.5 | c.1569G>T | p.Ala523= | synonymous_variant | 14/14 | 1 | |||
TH | ENST00000381175.5 | c.1557G>T | p.Ala519= | synonymous_variant | 14/14 | 1 | |||
TH | ENST00000333684.9 | c.1194G>T | p.Ala398= | synonymous_variant | 11/11 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000634 AC: 1AN: 157674Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 85054
GnomAD4 exome AF: 0.00000226 AC: 3AN: 1329918Hom.: 0 Cov.: 31 AF XY: 0.00000154 AC XY: 1AN XY: 650858
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Autosomal recessive DOPA responsive dystonia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at