rs3809997
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001308210.2(TSHZ1):āc.1524T>Cā(p.Pro508Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 1,613,950 control chromosomes in the GnomAD database, including 125,877 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.39 ( 11732 hom., cov: 33)
Exomes š: 0.39 ( 114145 hom. )
Consequence
TSHZ1
NM_001308210.2 synonymous
NM_001308210.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.29
Genes affected
TSHZ1 (HGNC:10669): (teashirt zinc finger homeobox 1) This gene encodes a colon cancer antigen that was defined by serological analysis of recombinant cDNA expression libraries. The encoded protein is a member of the teashirt C2H2-type zinc-finger protein family and may be involved in transcriptional regulation of developmental processes. Mutations in this gene may be associated with congenital aural atresia syndrome. [provided by RefSeq, Jan 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 18-75286931-T-C is Benign according to our data. Variant chr18-75286931-T-C is described in ClinVar as [Benign]. Clinvar id is 327819.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-75286931-T-C is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=-3.29 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TSHZ1 | NM_001308210.2 | c.1524T>C | p.Pro508Pro | synonymous_variant | 2/2 | ENST00000580243.3 | NP_001295139.1 | |
TSHZ1 | NM_005786.6 | c.1389T>C | p.Pro463Pro | synonymous_variant | 2/2 | NP_005777.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSHZ1 | ENST00000580243.3 | c.1524T>C | p.Pro508Pro | synonymous_variant | 2/2 | 2 | NM_001308210.2 | ENSP00000464391.1 | ||
TSHZ1 | ENST00000322038.5 | c.1389T>C | p.Pro463Pro | synonymous_variant | 2/2 | 1 | ENSP00000323584.5 | |||
TSHZ1 | ENST00000584217.1 | n.4068T>C | non_coding_transcript_exon_variant | 1/1 | 6 |
Frequencies
GnomAD3 genomes AF: 0.389 AC: 59146AN: 151978Hom.: 11725 Cov.: 33
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GnomAD3 exomes AF: 0.369 AC: 92604AN: 250962Hom.: 17842 AF XY: 0.374 AC XY: 50841AN XY: 135770
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GnomAD4 exome AF: 0.393 AC: 573864AN: 1461856Hom.: 114145 Cov.: 79 AF XY: 0.393 AC XY: 285692AN XY: 727222
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GnomAD4 genome AF: 0.389 AC: 59176AN: 152094Hom.: 11732 Cov.: 33 AF XY: 0.386 AC XY: 28732AN XY: 74342
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 17, 2021 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Aural atresia, congenital Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 10, 2021 | - - |
Computational scores
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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