rs11665337

Positions:

• chr18-77267680-G-A

Variant summary

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

The NM_001480.4(GALR1):​c.733-905G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0799 in 152,204 control chromosomes in the GnomAD database, including 557 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 0.080 (557 hom., cov: 32)
• Consequence: GALR1 NM_001480.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALR1	NM_001480.4	c.733-905G>A		intron_variant		ENST00000299727.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALR1	ENST00000299727.5	c.733-905G>A		intron_variant		1	NM_001480.4	P1

Frequencies

GnomAD3 genomes AF: 0.0799 AC: 12151 AN: 152086 Hom.: 556 Cov.: 32

Gnomad AFR AF: 0.0901

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.0704

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.0612

Gnomad SAS AF: 0.0454

Gnomad FIN AF: 0.0357

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0884

Gnomad OTH AF: 0.0758

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

GnomAD4 genome AF: 0.0799 AC: 12163 AN: 152204 Hom.: 557 Cov.: 32 AF XY: 0.0756 AC XY: 5625 AN XY: 74440

Gnomad4 AFR AF: 0.0902

Gnomad4 AMR AF: 0.0702

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.0616

Gnomad4 SAS AF: 0.0454

Gnomad4 FIN AF: 0.0357

Gnomad4 NFE AF: 0.0884

Gnomad4 OTH AF: 0.0745

Alfa AF: 0.0794 Hom.: 56

Bravo AF: 0.0823

Asia WGS AF: 0.0590 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.19

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: rs11665337; hg19: chr18-74979636;