rs2717164

Variant names:

• chr18-77256600-T-G
• rs2717164
• NM_001480.4:c.732+377T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GALR1	NM_001480.4	c.732+377T>G		intron_variant	Intron 2 of 2	ENST00000299727.5	NP_001471.2
GALR1	XM_017025691.2	c.732+377T>G		intron_variant	Intron 2 of 2		XP_016881180.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALR1	ENST00000299727.5	c.732+377T>G		intron_variant	Intron 2 of 2	1	NM_001480.4	ENSP00000299727.3

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

African (AFR) AF: 0.324 AC: 13435 AN: 41470

American (AMR) AF: 0.120 AC: 1835 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0709 AC: 246 AN: 3468

East Asian (EAS) AF: 0.177 AC: 915 AN: 5182

South Asian (SAS) AF: 0.169 AC: 818 AN: 4826

European-Finnish (FIN) AF: 0.0176 AC: 187 AN: 10614

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0170 AC: 1159 AN: 68020

Other (OTH) AF: 0.121 AC: 256 AN: 2108

Alfa AF: 0.102 Hom.: 355

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
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2717164; hg19: chr18-74968556;