chr7-30964346-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000823.4(GHRHR):c.57+221A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0754 in 152,142 control chromosomes in the GnomAD database, including 558 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.075 ( 558 hom., cov: 33)
Consequence
GHRHR
NM_000823.4 intron
NM_000823.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.990
Genes affected
GHRHR (HGNC:4266): (growth hormone releasing hormone receptor) This gene encodes a receptor for growth hormone-releasing hormone. Binding of this hormone to the receptor leads to synthesis and release of growth hormone. Mutations in this gene have been associated with isolated growth hormone deficiency (IGHD), also known as Dwarfism of Sindh, a disorder characterized by short stature. [provided by RefSeq, Jun 2010]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 7-30964346-A-G is Benign according to our data. Variant chr7-30964346-A-G is described in ClinVar as [Benign]. Clinvar id is 1281216.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| GHRHR | NM_000823.4 | c.57+221A>G | intron_variant | Intron 1 of 12 | ENST00000326139.7 | NP_000814.2 |
Ensembl
Frequencies
GnomAD3 genomes 0.0755 AC: 11473AN: 152024Hom.: 558 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
11473
AN:
152024
Hom.:
Cov.:
33
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 0.0754 AC: 11474AN: 152142Hom.: 558 Cov.: 33 AF XY: 0.0764 AC XY: 5682AN XY: 74376 show subpopulations
GnomAD4 genome
AF:
AC:
11474
AN:
152142
Hom.:
Cov.:
33
AF XY:
AC XY:
5682
AN XY:
74376
show subpopulations
African (AFR)
AF:
AC:
2003
AN:
41520
American (AMR)
AF:
AC:
1443
AN:
15302
Ashkenazi Jewish (ASJ)
AF:
AC:
745
AN:
3472
East Asian (EAS)
AF:
AC:
287
AN:
5154
South Asian (SAS)
AF:
AC:
748
AN:
4808
European-Finnish (FIN)
AF:
AC:
523
AN:
10604
Middle Eastern (MID)
AF:
AC:
63
AN:
294
European-Non Finnish (NFE)
AF:
AC:
5337
AN:
67966
Other (OTH)
AF:
AC:
240
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
545
1090
1635
2180
2725
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
304
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Nov 12, 2018
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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