chrX-624386-C-CT
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_006883.2(SHOX):c.-636dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.20 ( 4573 hom., 12183 hem., cov: 0)
Exomes 𝑓: 0.045 ( 0 hom. 1 hem. )
Consequence
SHOX
NM_006883.2 5_prime_UTR
NM_006883.2 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.14
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 -10 ACMG points.
BP6
Variant X-624386-C-CT is Benign according to our data. Variant chrX-624386-C-CT is described in ClinVar as [Benign]. Clinvar id is 3036689.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHOX | NM_006883.2 | c.-636dup | 5_prime_UTR_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHOX | ENST00000334060.8 | c.-636dup | 5_prime_UTR_variant | 1/6 | 5 | ||||
SHOX | ENST00000381578.6 | c.-636dup | 5_prime_UTR_variant | 1/6 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.195 AC: 25532AN: 130778Hom.: 4563 Cov.: 0 AF XY: 0.192 AC XY: 12152AN XY: 63160
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GnomAD4 exome AF: 0.0455 AC: 1AN: 22Hom.: 0 Cov.: 0 AF XY: 0.0833 AC XY: 1AN XY: 12
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GnomAD4 genome AF: 0.195 AC: 25564AN: 130816Hom.: 4573 Cov.: 0 AF XY: 0.193 AC XY: 12183AN XY: 63208
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SHOX-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 16, 2021 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at