rs2717164

chr18-77256600-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001480.4(GALR1):c.732+377T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,164 control chromosomes in the GnomAD database, including 2,543 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 0.12 (2543 hom., cov: 33)
• Consequence: GALR1 NM_001480.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALR1	NM_001480.4	c.732+377T>G		intron_variant		ENST00000299727.5
GALR1	XM_017025691.2	c.732+377T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALR1	ENST00000299727.5	c.732+377T>G		intron_variant		1	NM_001480.4	P1

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18849 AN: 152046 Hom.: 2530 Cov.: 33

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0176

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0171

Gnomad OTH AF: 0.121

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.124 AC: 18897 AN: 152164 Hom.: 2543 Cov.: 33 AF XY: 0.125 AC XY: 9326 AN XY: 74382

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.0709

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.0176

Gnomad4 NFE AF: 0.0170

Gnomad4 OTH AF: 0.121

Alfa AF: 0.0958 Hom.: 316

Bravo AF: 0.142

Asia WGS AF: 0.184 AC: 639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.9
Dann	Benign	0.42

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

Other links and lift over

dbSNP: rs2717164; hg19: chr18-74968556;