rs2717128

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001480.4(GALR1):​c.*6774A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,172 control chromosomes in the GnomAD database, including 1,532 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 0.14 ( 1532 hom., cov: 33)
Exomes 𝑓: 0.25 ( 0 hom. )

Consequence

GALR1
NM_001480.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.308
Variant links:
Genes affected
GALR1 (HGNC:4132): (galanin receptor 1) The neuropeptide galanin elicits a range of biological effects by interaction with specific G-protein-coupled receptors. Galanin receptors are seven-transmembrane proteins shown to activate a variety of intracellular second-messenger pathways. GALR1 inhibits adenylyl cyclase via a G protein of the Gi/Go family. GALR1 is widely expressed in the brain and spinal cord, as well as in peripheral sites such as the small intestine and heart. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GALR1NM_001480.4 linkuse as main transcriptc.*6774A>G 3_prime_UTR_variant 3/3 ENST00000299727.5 NP_001471.2 P47211

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GALR1ENST00000299727.5 linkuse as main transcriptc.*6774A>G 3_prime_UTR_variant 3/31 NM_001480.4 ENSP00000299727.3 P47211

Frequencies

GnomAD3 genomes
AF:
0.138
AC:
21001
AN:
152050
Hom.:
1522
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.156
Gnomad AMI
AF:
0.125
Gnomad AMR
AF:
0.167
Gnomad ASJ
AF:
0.0611
Gnomad EAS
AF:
0.142
Gnomad SAS
AF:
0.0803
Gnomad FIN
AF:
0.125
Gnomad MID
AF:
0.0854
Gnomad NFE
AF:
0.132
Gnomad OTH
AF:
0.125
GnomAD4 exome
AF:
0.250
AC:
1
AN:
4
Hom.:
0
Cov.:
0
AF XY:
0.500
AC XY:
1
AN XY:
2
show subpopulations
Gnomad4 EAS exome
AF:
0.500
Gnomad4 NFE exome
AF:
0.00
GnomAD4 genome
AF:
0.138
AC:
21034
AN:
152168
Hom.:
1532
Cov.:
33
AF XY:
0.137
AC XY:
10179
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.156
Gnomad4 AMR
AF:
0.167
Gnomad4 ASJ
AF:
0.0611
Gnomad4 EAS
AF:
0.142
Gnomad4 SAS
AF:
0.0803
Gnomad4 FIN
AF:
0.125
Gnomad4 NFE
AF:
0.132
Gnomad4 OTH
AF:
0.124
Alfa
AF:
0.132
Hom.:
2826
Bravo
AF:
0.143
Asia WGS
AF:
0.120
AC:
420
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
1.8
DANN
Benign
0.46

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: rs2717128; hg19: chr18-74987632; API