rs696217

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_016362.5(GHRL):​c.214C>G​(p.Leu72Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000689 in 1,451,160 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)
Exomes š‘“: 6.9e-7 ( 0 hom. )

Consequence

GHRL
NM_016362.5 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.30
Variant links:
Genes affected
GHRL (HGNC:18129): (ghrelin and obestatin prepropeptide) This gene encodes the ghrelin-obestatin preproprotein that is cleaved to yield two peptides, ghrelin and obestatin. Ghrelin is a powerful appetite stimulant and plays an important role in energy homeostasis. Its secretion is initiated when the stomach is empty, whereupon it binds to the growth hormone secretagogue receptor in the hypothalamus which results in the secretion of growth hormone (somatotropin). Ghrelin is thought to regulate multiple activities, including hunger, reward perception via the mesolimbic pathway, gastric acid secretion, gastrointestinal motility, and pancreatic glucose-stimulated insulin secretion. It was initially proposed that obestatin plays an opposing role to ghrelin by promoting satiety and thus decreasing food intake, but this action is still debated. Recent reports suggest multiple metabolic roles for obestatin, including regulating adipocyte function and glucose metabolism. Alternative splicing results in multiple transcript variants. In addition, antisense transcripts for this gene have been identified and may potentially regulate ghrelin-obestatin preproprotein expression. [provided by RefSeq, Nov 2014]
GHRLOS (HGNC:33885): (ghrelin opposite strand/antisense RNA) This gene is an antisense gene of the ghrelin/obestatin prepropeptide gene. Alternatively spliced transcript variants have been identified and they may function as non-coding regulatory RNAs. [provided by RefSeq, Jan 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.27436188).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GHRLNM_016362.5 linkc.214C>G p.Leu72Val missense_variant Exon 4 of 6 ENST00000335542.13 NP_057446.1 Q9UBU3-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GHRLENST00000335542.13 linkc.214C>G p.Leu72Val missense_variant Exon 4 of 6 1 NM_016362.5 ENSP00000335074.8 Q9UBU3-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
6.89e-7
AC:
1
AN:
1451160
Hom.:
0
Cov.:
30
AF XY:
0.00000138
AC XY:
1
AN XY:
722686
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.07e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.067
T
BayesDel_noAF
Benign
-0.33
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.11
T;.;.;.;.;.;T;T
Eigen
Uncertain
0.30
Eigen_PC
Benign
0.20
FATHMM_MKL
Uncertain
0.79
D
LIST_S2
Benign
0.80
.;.;T;D;T;D;.;D
M_CAP
Benign
0.016
T
MetaRNN
Benign
0.27
T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.82
T
MutationAssessor
Benign
1.8
L;.;L;.;.;.;L;L
PrimateAI
Benign
0.43
T
PROVEAN
Benign
-0.77
N;N;N;N;N;N;N;N
REVEL
Benign
0.061
Sift
Benign
0.16
T;T;D;T;T;T;T;T
Sift4G
Benign
0.36
T;T;D;D;D;T;T;T
Polyphen
1.0
D;D;.;D;D;D;D;D
Vest4
0.43
MutPred
0.32
Loss of sheet (P = 0.0228);.;Loss of sheet (P = 0.0228);.;.;.;Loss of sheet (P = 0.0228);Loss of sheet (P = 0.0228);
MVP
0.53
MPC
0.032
ClinPred
0.76
D
GERP RS
3.4
Varity_R
0.095
gMVP
0.14

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-10331457; API