5-42714748-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000163.5(GHR):c.875+1229T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,012 control chromosomes in the GnomAD database, including 34,488 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.66 (34488 hom., cov: 32)
• Consequence: GHR NM_000163.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GHR	NM_000163.5	c.875+1229T>C		intron_variant		ENST00000230882.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GHR	ENST00000230882.9	c.875+1229T>C		intron_variant		1	NM_000163.5	P1

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100529 AN: 151894 Hom.: 34471 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.658

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.662 AC: 100577 AN: 152012 Hom.: 34488 Cov.: 32 AF XY: 0.664 AC XY: 49367 AN XY: 74294

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.734

Gnomad4 OTH AF: 0.660

Alfa AF: 0.687 Hom.: 4556

Bravo AF: 0.657

Asia WGS AF: 0.764 AC: 2640 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.87
Dann	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2972780; hg19: chr5-42714850;