rs16997525
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_173485.6(TSHZ2):c.40+130550T>C variant causes a intron change. The variant allele was found at a frequency of 0.195 in 152,184 control chromosomes in the GnomAD database, including 3,620 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.20 ( 3620 hom., cov: 32)
Consequence
TSHZ2
NM_173485.6 intron
NM_173485.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.70
Genes affected
TSHZ2 (HGNC:13010): (teashirt zinc finger homeobox 2) This gene is a member of the teashirt C2H2-type zinc-finger protein family of transcription factors. This gene encodes a protein with five C2H2-type zinc fingers, a homeobox DNA-binding domain and a coiled-coil domain. This nuclear protein is predicted to act as a transcriptional repressor. This gene is thought to play a role in the development and progression of breast and other types of cancer. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.29).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSHZ2 | NM_173485.6 | c.40+130550T>C | intron_variant | ENST00000371497.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSHZ2 | ENST00000371497.10 | c.40+130550T>C | intron_variant | 1 | NM_173485.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.195 AC: 29647AN: 152066Hom.: 3611 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.195 AC: 29686AN: 152184Hom.: 3620 Cov.: 32 AF XY: 0.193 AC XY: 14383AN XY: 74426
GnomAD4 genome
?
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29686
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32
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14383
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74426
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Asia WGS
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509
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at