NM_000163.5:c.-12+259_-12+264dupGTGTGT
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_000163.5(GHR):c.-12+259_-12+264dupGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.094 ( 796 hom., cov: 0)
Consequence
GHR
NM_000163.5 intron
NM_000163.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.21
Publications
0 publications found
Genes affected
GHR (HGNC:4263): (growth hormone receptor) This gene encodes a member of the type I cytokine receptor family, which is a transmembrane receptor for growth hormone. Binding of growth hormone to the receptor leads to receptor dimerization and the activation of an intra- and intercellular signal transduction pathway leading to growth. Mutations in this gene have been associated with Laron syndrome, also known as the growth hormone insensitivity syndrome (GHIS), a disorder characterized by short stature. In humans and rabbits, but not rodents, growth hormone binding protein (GHBP) is generated by proteolytic cleavage of the extracellular ligand-binding domain from the mature growth hormone receptor protein. Multiple alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Jun 2011]
GHR Gene-Disease associations (from GenCC):
- Laron syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P
- short stature due to partial GHR deficiencyInheritance: Unknown, AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP6
Variant 5-42424171-A-AGTGTGT is Benign according to our data. Variant chr5-42424171-A-AGTGTGT is described in ClinVar as [Benign]. Clinvar id is 1290974.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.0934 AC: 9378AN: 100366Hom.: 793 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
9378
AN:
100366
Hom.:
Cov.:
0
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.0935 AC: 9392AN: 100434Hom.: 796 Cov.: 0 AF XY: 0.0918 AC XY: 4285AN XY: 46674 show subpopulations
GnomAD4 genome
AF:
AC:
9392
AN:
100434
Hom.:
Cov.:
0
AF XY:
AC XY:
4285
AN XY:
46674
show subpopulations
African (AFR)
AF:
AC:
2008
AN:
24198
American (AMR)
AF:
AC:
722
AN:
10332
Ashkenazi Jewish (ASJ)
AF:
AC:
362
AN:
2656
East Asian (EAS)
AF:
AC:
449
AN:
3210
South Asian (SAS)
AF:
AC:
275
AN:
2516
European-Finnish (FIN)
AF:
AC:
448
AN:
4938
Middle Eastern (MID)
AF:
AC:
19
AN:
188
European-Non Finnish (NFE)
AF:
AC:
4982
AN:
50330
Other (OTH)
AF:
AC:
111
AN:
1368
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.518
Heterozygous variant carriers
0
350
700
1050
1400
1750
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jun 19, 2021
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.