rs2972418

Positions:

• chr5-42483591-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.-12+59636T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,980 control chromosomes in the GnomAD database, including 20,763 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 0.51 (20763 hom., cov: 31)
• Consequence: GHR NM_000163.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GHR	NM_000163.5	c.-12+59636T>C		intron_variant		ENST00000230882.9
GHR	NM_001242399.2	c.10+58993T>C		intron_variant
GHR	NM_001242400.2	c.-296-30489T>C		intron_variant
GHR	NM_001242401.4	c.-12+262T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GHR	ENST00000230882.9	c.-12+59636T>C		intron_variant		1	NM_000163.5	P1
GHR	ENST00000615111.4	c.-296-30489T>C		intron_variant		5		P1
GHR	ENST00000620156.4	c.10+58993T>C		intron_variant		5
GHR	ENST00000513671.5	c.-12+58993T>C		intron_variant, NMD_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77466 AN: 151864 Hom.: 20745 Cov.: 31

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.510 AC: 77525 AN: 151980 Hom.: 20763 Cov.: 31 AF XY: 0.505 AC XY: 37487 AN XY: 74280

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.526

Alfa AF: 0.486 Hom.: 37144

Bravo AF: 0.520

Asia WGS AF: 0.271 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.26

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: rs2972418; hg19: chr5-42483693;