rs2850878

Variant names:

• chr18-77257706-G-A
• rs2850878
• NM_001480.4:c.732+1483G>A

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+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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• 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=-0.83).
• 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 rank	MANE	Protein	UniProt
GALR1	NM_001480.4	c.732+1483G>A		intron_variant	Intron 2 of 2	ENST00000299727.5	NP_001471.2
GALR1	XM_017025691.2	c.732+1483G>A		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+1483G>A		intron_variant	Intron 2 of 2	1	NM_001480.4	ENSP00000299727.3

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119607 AN: 152026 Hom.: 47150 Cov.: 33

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

African (AFR) AF: 0.804 AC: 33390 AN: 41520

American (AMR) AF: 0.816 AC: 12473 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3053 AN: 3472

East Asian (EAS) AF: 0.659 AC: 3405 AN: 5168

South Asian (SAS) AF: 0.706 AC: 3404 AN: 4824

European-Finnish (FIN) AF: 0.768 AC: 8122 AN: 10576

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.782 AC: 53185 AN: 67976

Other (OTH) AF: 0.789 AC: 1666 AN: 2112

Alfa AF: 0.781 Hom.: 27230

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
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2850878; hg19: chr18-74969662;