5-42667769-T-C

Position:

• chr5-42667769-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.137-21121T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,128 control chromosomes in the GnomAD database, including 52,550 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 0.83 (52550 hom., cov: 31)
• Consequence: GHR NM_000163.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GHR	NM_000163.5	c.137-21121T>C		intron_variant		ENST00000230882.9	NP_000154.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GHR	ENST00000230882.9	c.137-21121T>C		intron_variant		1	NM_000163.5	ENSP00000230882	P1

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126061 AN: 152010 Hom.: 52519 Cov.: 31

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.829 AC: 126143 AN: 152128 Hom.: 52550 Cov.: 31 AF XY: 0.832 AC XY: 61894 AN XY: 74382

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.904

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.934

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.837

Gnomad4 OTH AF: 0.835

Alfa AF: 0.844 Hom.: 106786

Bravo AF: 0.830

Asia WGS AF: 0.958 AC: 3329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.68
DANN	Benign	0.31

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: rs6878512; hg19: chr5-42667871;