rs4988504
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000823.4(GHRHR):c.975-26G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 1,606,386 control chromosomes in the GnomAD database, including 9,664 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). There are indicators that this mutation may affect the branch point..
Frequency
Genomes: 𝑓 0.11 ( 913 hom., cov: 32)
Exomes 𝑓: 0.11 ( 8751 hom. )
Consequence
GHRHR
NM_000823.4 intron
NM_000823.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.447
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 made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
This place is a probable branch point but likely benign (scored 1 / 10). Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 7-30976403-G-A is Benign according to our data. Variant chr7-30976403-G-A is described in ClinVar as [Benign]. Clinvar id is 1226509.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GHRHR | NM_000823.4 | c.975-26G>A | intron_variant | ENST00000326139.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GHRHR | ENST00000326139.7 | c.975-26G>A | intron_variant | 1 | NM_000823.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.106 AC: 16056AN: 152040Hom.: 918 Cov.: 32
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GnomAD3 exomes AF: 0.116 AC: 29055AN: 251018Hom.: 1800 AF XY: 0.115 AC XY: 15648AN XY: 135700
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GnomAD4 exome AF: 0.106 AC: 154043AN: 1454228Hom.: 8751 Cov.: 30 AF XY: 0.107 AC XY: 77555AN XY: 723876
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GnomAD4 genome ? AF: 0.105 AC: 16042AN: 152158Hom.: 913 Cov.: 32 AF XY: 0.105 AC XY: 7775AN XY: 74388
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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 | Nov 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
BranchPoint Hunter
?
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