rs2850878

Variant summary

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

The NM_001480.4(GALR1):​c.732+1483G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 152,144 control chromosomes in the GnomAD database, including 47,184 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 0.79 ( 47184 hom., cov: 33)

Consequence

GALR1
NM_001480.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.280
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=-0.83).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GALR1NM_001480.4 linkuse as main transcriptc.732+1483G>A intron_variant ENST00000299727.5
GALR1XM_017025691.2 linkuse as main transcriptc.732+1483G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GALR1ENST00000299727.5 linkuse as main transcriptc.732+1483G>A intron_variant 1 NM_001480.4 P1

Frequencies

GnomAD3 genomes
AF:
0.787
AC:
119607
AN:
152026
Hom.:
47150
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.804
Gnomad AMI
AF:
0.838
Gnomad AMR
AF:
0.816
Gnomad ASJ
AF:
0.879
Gnomad EAS
AF:
0.659
Gnomad SAS
AF:
0.707
Gnomad FIN
AF:
0.768
Gnomad MID
AF:
0.794
Gnomad NFE
AF:
0.782
Gnomad OTH
AF:
0.795
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.787
AC:
119694
AN:
152144
Hom.:
47184
Cov.:
33
AF XY:
0.787
AC XY:
58503
AN XY:
74374
show subpopulations
Gnomad4 AFR
AF:
0.804
Gnomad4 AMR
AF:
0.816
Gnomad4 ASJ
AF:
0.879
Gnomad4 EAS
AF:
0.659
Gnomad4 SAS
AF:
0.706
Gnomad4 FIN
AF:
0.768
Gnomad4 NFE
AF:
0.782
Gnomad4 OTH
AF:
0.789
Alfa
AF:
0.780
Hom.:
24846
Bravo
AF:
0.793
Asia WGS
AF:
0.682
AC:
2372
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
4.1
DANN
Benign
0.78

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.050
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: rs2850878; hg19: chr18-74969662; API