rs369390009
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_000451.4(SHOX):c.*284_*285dup variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 432,518 control chromosomes in the GnomAD database, including 6,669 homozygotes. There are 36,827 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: 𝑓 0.16 ( 2073 hom., 11624 hem., cov: 29)
Exomes 𝑓: 0.18 ( 4596 hom. 25203 hem. )
Consequence
SHOX
NM_000451.4 3_prime_UTR
NM_000451.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.336
Genes affected
SHOX (HGNC:10853): (SHOX homeobox) This gene belongs to the paired homeobox family and is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes. Defects in this gene are associated with idiopathic growth retardation and in the short stature phenotype of Turner syndrome patients. This gene is highly conserved across species from mammals to fish to flies. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHOX | NM_000451.4 | c.*284_*285dup | 3_prime_UTR_variant | 5/5 | ENST00000686671.1 | ||
SHOX | NM_006883.2 | c.633+3833_633+3834dup | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHOX | ENST00000686671.1 | c.*284_*285dup | 3_prime_UTR_variant | 5/5 | NM_000451.4 | P1 | |||
SHOX | ENST00000381575.6 | c.633+3833_633+3834dup | intron_variant | 1 | |||||
SHOX | ENST00000381578.6 | c.*284_*285dup | 3_prime_UTR_variant | 6/6 | 5 | P1 | |||
SHOX | ENST00000334060.8 | c.633+3833_633+3834dup | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.159 AC: 24110AN: 151980Hom.: 2072 Cov.: 29 AF XY: 0.156 AC XY: 11612AN XY: 74222
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?
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GnomAD4 exome AF: 0.176 AC: 49285AN: 280420Hom.: 4596 Cov.: 3 AF XY: 0.176 AC XY: 25203AN XY: 143316
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GnomAD4 genome ? AF: 0.159 AC: 24115AN: 152098Hom.: 2073 Cov.: 29 AF XY: 0.156 AC XY: 11624AN XY: 74350
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
SHOX-related short stature Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Human Genetics Disease in Children – Taif University, Taif University | Mar 03, 2016 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at