chr18-77271099-A-G

Variant summary

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

The NM_001480.4(GALR1):​c.*2197A>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 0.067 in 152,184 control chromosomes in the GnomAD database, including 431 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 0.067 ( 431 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

GALR1
NM_001480.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0720
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=-0.88).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0977 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GALR1NM_001480.4 linkuse as main transcriptc.*2197A>G 3_prime_UTR_variant 3/3 ENST00000299727.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GALR1ENST00000299727.5 linkuse as main transcriptc.*2197A>G 3_prime_UTR_variant 3/31 NM_001480.4 P1

Frequencies

GnomAD3 genomes
AF:
0.0669
AC:
10173
AN:
152066
Hom.:
422
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0965
Gnomad AMI
AF:
0.0562
Gnomad AMR
AF:
0.102
Gnomad ASJ
AF:
0.00894
Gnomad EAS
AF:
0.0797
Gnomad SAS
AF:
0.0334
Gnomad FIN
AF:
0.0915
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.0422
Gnomad OTH
AF:
0.0588
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
2
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
2
Gnomad4 NFE exome
AF:
0.00
GnomAD4 genome
AF:
0.0670
AC:
10203
AN:
152184
Hom.:
431
Cov.:
32
AF XY:
0.0701
AC XY:
5216
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.0968
Gnomad4 AMR
AF:
0.102
Gnomad4 ASJ
AF:
0.00894
Gnomad4 EAS
AF:
0.0797
Gnomad4 SAS
AF:
0.0334
Gnomad4 FIN
AF:
0.0915
Gnomad4 NFE
AF:
0.0422
Gnomad4 OTH
AF:
0.0591
Alfa
AF:
0.0482
Hom.:
107
Bravo
AF:
0.0702
Asia WGS
AF:
0.0620
AC:
219
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
2.0
DANN
Benign
0.65

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: rs8097893; hg19: chr18-74983055; API