17-76074894-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_003857.4(GALR2):​c.11C>T​(p.Ser4Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000321 in 1,528,066 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00024 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000094 ( 0 hom. )

Consequence

GALR2
NM_003857.4 missense

Scores

1
4
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.481
Variant links:
Genes affected
GALR2 (HGNC:4133): (galanin receptor 2) Galanin is an important neuromodulator present in the brain, gastrointestinal system, and hypothalamopituitary axis. It is a 30-amino acid non-C-terminally amidated peptide that potently stimulates growth hormone secretion, inhibits cardiac vagal slowing of heart rate, abolishes sinus arrhythmia, and inhibits postprandial gastrointestinal motility. The actions of galanin are mediated through interaction with specific membrane receptors that are members of the 7-transmembrane family of G protein-coupled receptors. GALR2 interacts with the N-terminal residues of the galanin peptide. The primary signaling mechanism for GALR2 is through the phospholipase C/protein kinase C pathway (via Gq), in contrast to GALR1, which communicates its intracellular signal by inhibition of adenylyl cyclase through Gi. However, it has been demonstrated that GALR2 couples efficiently to both the Gq and Gi proteins to simultaneously activate 2 independent signal transduction pathways. [provided by RefSeq, Jul 2008]
ZACN (HGNC:29504): (zinc activated ion channel) LGICZ1 is a zinc-activated ligand-gated ion channel that defines a new subgroup of the cysteine-loop superfamily of ligand-gated ion channels (Davies et al., 2003 [PubMed 12381728]).[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.02836591).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GALR2NM_003857.4 linkc.11C>T p.Ser4Leu missense_variant Exon 1 of 2 ENST00000329003.4 NP_003848.1 O43603
GALR2XM_011525427.4 linkc.76-236C>T intron_variant Intron 2 of 3 XP_011523729.1
GALR2XM_047436984.1 linkc.76-236C>T intron_variant Intron 2 of 3 XP_047292940.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GALR2ENST00000329003.4 linkc.11C>T p.Ser4Leu missense_variant Exon 1 of 2 1 NM_003857.4 ENSP00000329684.3 O43603
ZACNENST00000591500.1 linkn.216+2718C>T intron_variant Intron 1 of 1 4

Frequencies

GnomAD3 genomes
AF:
0.000230
AC:
35
AN:
152194
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000844
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000305
AC:
4
AN:
131322
Hom.:
0
AF XY:
0.0000141
AC XY:
1
AN XY:
71052
show subpopulations
Gnomad AFR exome
AF:
0.000434
Gnomad AMR exome
AF:
0.0000411
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000945
AC:
13
AN:
1375754
Hom.:
0
Cov.:
32
AF XY:
0.0000103
AC XY:
7
AN XY:
678126
show subpopulations
Gnomad4 AFR exome
AF:
0.000191
Gnomad4 AMR exome
AF:
0.0000565
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:
0.00000372
Gnomad4 OTH exome
AF:
0.0000174
GnomAD4 genome
AF:
0.000236
AC:
36
AN:
152312
Hom.:
0
Cov.:
32
AF XY:
0.000255
AC XY:
19
AN XY:
74490
show subpopulations
Gnomad4 AFR
AF:
0.000866
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000712
Hom.:
0
Bravo
AF:
0.000140
ExAC
AF:
0.0000486
AC:
5

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Dec 20, 2023
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.11C>T (p.S4L) alteration is located in exon 1 (coding exon 1) of the GALR2 gene. This alteration results from a C to T substitution at nucleotide position 11, causing the serine (S) at amino acid position 4 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.15
BayesDel_addAF
Benign
-0.49
T
BayesDel_noAF
Benign
-0.50
CADD
Benign
21
DANN
Uncertain
1.0
DEOGEN2
Benign
0.099
T
Eigen
Benign
-0.87
Eigen_PC
Benign
-0.93
FATHMM_MKL
Benign
0.39
N
LIST_S2
Benign
0.58
T
M_CAP
Uncertain
0.090
D
MetaRNN
Benign
0.028
T
MetaSVM
Benign
-0.85
T
MutationAssessor
Benign
1.3
L
PrimateAI
Uncertain
0.69
T
PROVEAN
Benign
-0.80
N
REVEL
Benign
0.077
Sift
Uncertain
0.0040
D
Sift4G
Pathogenic
0.0
D
Polyphen
0.0080
B
Vest4
0.17
MVP
0.72
ClinPred
0.051
T
GERP RS
0.46
Varity_R
0.14
gMVP
0.64

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs150585267; hg19: chr17-74070975; API