chr18-75285574-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001308210.2(TSHZ1):c.167C>T(p.Ala56Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000625 in 1,599,732 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A56A) has been classified as Likely benign.
Frequency
Consequence
NM_001308210.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSHZ1 | NM_001308210.2 | c.167C>T | p.Ala56Val | missense_variant | 2/2 | ENST00000580243.3 | |
TSHZ1 | NM_005786.6 | c.32C>T | p.Ala11Val | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSHZ1 | ENST00000580243.3 | c.167C>T | p.Ala56Val | missense_variant | 2/2 | 2 | NM_001308210.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000122 AC: 3AN: 246650Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133436
GnomAD4 exome AF: 0.00000553 AC: 8AN: 1447626Hom.: 0 Cov.: 32 AF XY: 0.00000139 AC XY: 1AN XY: 717364
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 14, 2021 | The c.32C>T (p.A11V) alteration is located in exon 2 (coding exon 1) of the TSHZ1 gene. This alteration results from a C to T substitution at nucleotide position 32, causing the alanine (A) at amino acid position 11 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at