chr15-43370961-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001372080.1(ZSCAN29):c.-516C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00762 in 180,664 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.011 ( 18 hom., cov: 32)
Exomes 𝑓: 0.0017 ( 2 hom. )
Consequence
ZSCAN29
NM_001372080.1 5_prime_UTR
NM_001372080.1 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.19
Genes affected
ZSCAN29 (HGNC:26673): (zinc finger and SCAN domain containing 29) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
TUBGCP4 (HGNC:16691): (tubulin gamma complex component 4) This gene encodes a component of the gamma-tubulin ring complex, which is required for microtubule nucleation. In mammalian cells, the protein localizes to centrosomes in association with gamma-tubulin. Crystal structure analysis revealed a structure composed of five helical bundles arranged around conserved hydrophobic cores. An exposed surface area located in the C-terminal domain is essential and sufficient for direct binding to gamma-tubulin. Mutations in this gene that alter microtubule organization are associated with microcephaly and chorioretinopathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 15-43370961-G-C is Benign according to our data. Variant chr15-43370961-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1188532.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0112 (1263/112644) while in subpopulation AFR AF= 0.0362 (1195/32994). AF 95% confidence interval is 0.0345. There are 18 homozygotes in gnomad4. There are 593 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 18 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZSCAN29 | NM_001372080.1 | c.-516C>G | 5_prime_UTR_variant | 1/6 | ENST00000684362.1 | ||
ZSCAN29 | XM_047432187.1 | c.-836C>G | 5_prime_UTR_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZSCAN29 | ENST00000684362.1 | c.-516C>G | 5_prime_UTR_variant | 1/6 | NM_001372080.1 | P1 | |||
TUBGCP4 | ENST00000570081.1 | n.293+1259G>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0112 AC: 1257AN: 112584Hom.: 18 Cov.: 32
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GnomAD4 exome AF: 0.00168 AC: 114AN: 68020Hom.: 2 Cov.: 0 AF XY: 0.00155 AC XY: 57AN XY: 36708
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GnomAD4 genome ? AF: 0.0112 AC: 1263AN: 112644Hom.: 18 Cov.: 32 AF XY: 0.0108 AC XY: 593AN XY: 54718
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 07, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at