chrX-624386-C-CTT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_006883.2(SHOX):c.-637_-636dup 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 0.29 ( 5071 hom., 18302 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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant X-624386-C-CTT is Benign according to our data. Variant chrX-624386-C-CTT is described in ClinVar as [Likely_benign]. Clinvar id is 3036935.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHOX | NM_006883.2 | c.-637_-636dup | 5_prime_UTR_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHOX | ENST00000334060.8 | c.-637_-636dup | 5_prime_UTR_variant | 1/6 | 5 | ||||
SHOX | ENST00000381578.6 | c.-637_-636dup | 5_prime_UTR_variant | 1/6 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.289 AC: 37782AN: 130528Hom.: 5067 Cov.: 0 AF XY: 0.290 AC XY: 18292AN XY: 63022
GnomAD3 genomes
?
AF:
AC:
37782
AN:
130528
Hom.:
Cov.:
0
AF XY:
AC XY:
18292
AN XY:
63022
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0455 AC: 1AN: 22Hom.: 0 Cov.: 0 AF XY: 0.0833 AC XY: 1AN XY: 12
GnomAD4 exome
AF:
AC:
1
AN:
22
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
12
Gnomad4 AFR exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.289 AC: 37793AN: 130564Hom.: 5071 Cov.: 0 AF XY: 0.290 AC XY: 18302AN XY: 63068
GnomAD4 genome
?
AF:
AC:
37793
AN:
130564
Hom.:
Cov.:
0
AF XY:
AC XY:
18302
AN XY:
63068
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
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 | Feb 16, 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
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at