5-42424171-AGTGTGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGTGTGTGT

Variant names:

• chr5-42424171-AGTGTGTGTGT-A
• rs1158830359
• NM_000163.5:c.-12+255_-12+264delGTGTGTGTGT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_000163.5(GHR):​c.-12+255_-12+264delGTGTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.071 (256 hom., cov: 0)
• Consequence: GHR NM_000163.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• 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 syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P
• short stature due to partial GHR deficiency

  Inheritance: AD, Unknown Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0834 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000163.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GHR	NM_000163.5	MANE Select	c.-12+255_-12+264delGTGTGTGTGT		intron	N/A	NP_000154.1	P10912-1
	GHR	NM_001242460.2		c.-12+255_-12+264delGTGTGTGTGT		intron	N/A	NP_001229389.1	P10912-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GHR	ENST00000230882.9	TSL:1 MANE Select	c.-12+217_-12+226delGTGTGTGTGT		intron	N/A	ENSP00000230882.4	P10912-1
	GHR	ENST00000887691.1		c.-531_-522delGTGTGTGTGT		5_prime_UTR	Exon 1 of 11	ENSP00000557750.1
	GHR	ENST00000887685.1		c.-368+217_-368+226delGTGTGTGTGT		intron	N/A	ENSP00000557744.1

Frequencies

GnomAD3 genomes AF: 0.0709 AC: 7126 AN: 100492 Hom.: 257 Cov.: 0

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.0626

Gnomad ASJ AF: 0.0809

Gnomad EAS AF: 0.00402

Gnomad SAS AF: 0.0663

Gnomad FIN AF: 0.0894

Gnomad MID AF: 0.0990

Gnomad NFE AF: 0.0855

Gnomad OTH AF: 0.0838

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

GnomAD4 genome AF: 0.0708 AC: 7124 AN: 100560 Hom.: 256 Cov.: 0 AF XY: 0.0700 AC XY: 3270 AN XY: 46742

African (AFR) AF: 0.0458 AC: 1109 AN: 24216

American (AMR) AF: 0.0626 AC: 648 AN: 10352

Ashkenazi Jewish (ASJ) AF: 0.0809 AC: 215 AN: 2658

East Asian (EAS) AF: 0.00404 AC: 13 AN: 3218

South Asian (SAS) AF: 0.0655 AC: 165 AN: 2518

European-Finnish (FIN) AF: 0.0894 AC: 443 AN: 4954

Middle Eastern (MID) AF: 0.0938 AC: 18 AN: 192

European-Non Finnish (NFE) AF: 0.0855 AC: 4307 AN: 50382

Other (OTH) AF: 0.0824 AC: 113 AN: 1372

Alfa AF: 0.00 Hom.: 144

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1158830359;

hg19: chr5-42424273;