chrX-630307-A-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006883.2(SHOX):c.-432-159A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 151,264 control chromosomes in the GnomAD database, including 40,026 homozygotes. There are 53,619 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.72 ( 40026 hom., 53619 hem., cov: 32)
Consequence
SHOX
NM_006883.2 intron
NM_006883.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.32
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant X-630307-A-G is Benign according to our data. Variant chrX-630307-A-G is described in ClinVar as [Benign]. Clinvar id is 1239870.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-630307-A-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHOX | NM_006883.2 | c.-432-159A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHOX | ENST00000334060.8 | c.-432-159A>G | intron_variant | 5 | |||||
SHOX | ENST00000381578.6 | c.-432-159A>G | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.725 AC: 109570AN: 151142Hom.: 39999 Cov.: 32 AF XY: 0.726 AC XY: 53536AN XY: 73748
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.725 AC: 109649AN: 151264Hom.: 40026 Cov.: 32 AF XY: 0.726 AC XY: 53619AN XY: 73878
GnomAD4 genome
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at