22-37825261-G-T
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003614.2(GALR3):c.898G>T(p.Ala300Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000709 in 1,409,746 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 34)
Exomes 𝑓: 0.0000063 ( 0 hom. )
Consequence
GALR3
NM_003614.2 missense
NM_003614.2 missense
Scores
2
3
14
Clinical Significance
Conservation
PhyloP100: 4.33
Genes affected
GALR3 (HGNC:4134): (galanin receptor 3) The neuropeptide galanin modulates a variety of physiologic processes including cognition/memory, sensory/pain processing, hormone secretion, and feeding behavior. The human galanin receptors are G protein-coupled receptors that functionally couple to their intracellular effector through distinct signaling pathways. GALR3 is found in many tissues and may be expressed as 1.4-, 2.4-, and 5-kb transcripts [provided by RefSeq, Jul 2008]
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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=0.2764786).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALR3 | NM_003614.2 | c.898G>T | p.Ala300Ser | missense_variant | 2/2 | ENST00000249041.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALR3 | ENST00000249041.3 | c.898G>T | p.Ala300Ser | missense_variant | 2/2 | 1 | NM_003614.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000134 AC: 2AN: 149500Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.00000704 AC: 1AN: 141956Hom.: 0 AF XY: 0.0000121 AC XY: 1AN XY: 82430
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GnomAD4 exome AF: 0.00000635 AC: 8AN: 1260246Hom.: 0 Cov.: 33 AF XY: 0.00000640 AC XY: 4AN XY: 625340
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GnomAD4 genome AF: 0.0000134 AC: 2AN: 149500Hom.: 0 Cov.: 34 AF XY: 0.0000274 AC XY: 2AN XY: 72888
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.898G>T (p.A300S) alteration is located in exon 2 (coding exon 2) of the GALR3 gene. This alteration results from a G to T substitution at nucleotide position 898, causing the alanine (A) at amino acid position 300 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
N
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
P
Vest4
MutPred
Gain of glycosylation at A300 (P = 0.0155);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at