chrX-624387-T-TTTG
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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.-646_-645insGTT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.58 ( 6271 hom., 19293 hem., cov: 0)
Exomes 𝑓: 0.23 ( 0 hom. 2 hem. )
Failed GnomAD Quality Control
Consequence
SHOX
NM_006883.2 5_prime_UTR
NM_006883.2 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.08
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-624387-T-TTTG is Benign according to our data. Variant chrX-624387-T-TTTG is described in ClinVar as [Likely_benign]. Clinvar id is 3036731.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0759 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHOX | NM_006883.2 | c.-646_-645insGTT | 5_prime_UTR_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHOX | ENST00000334060.8 | c.-646_-645insGTT | 5_prime_UTR_variant | 1/6 | 5 | ||||
SHOX | ENST00000381578.6 | c.-646_-645insGTT | 5_prime_UTR_variant | 1/6 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 39849AN: 68864Hom.: 6276 Cov.: 0 AF XY: 0.579 AC XY: 19298AN XY: 33322 FAILED QC
GnomAD3 genomes
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GnomAD4 exome AF: 0.227 AC: 5AN: 22Hom.: 0 Cov.: 0 AF XY: 0.143 AC XY: 2AN XY: 14
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GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.579 AC: 39827AN: 68830Hom.: 6271 Cov.: 0 AF XY: 0.579 AC XY: 19293AN XY: 33314
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Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SHOX-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 04, 2021 | This variant is classified as likely 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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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at