14-105049889-C-T

Position:

• chr14-105049889-C-T

Variant summary

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

The NM_013345.4(GPR132):​c.*1105G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,320 control chromosomes in the GnomAD database, including 22,284 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 0.51 (22264 hom., cov: 34)
  • Exomes 𝑓: 0.61 (20 hom.)
• Consequence: GPR132 NM_013345.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556

Genes affected

GPR132 (HGNC:17482): (G protein-coupled receptor 132) This gene encodes a member of the guanine nucleotide-binding protein (G protein)-coupled receptor (GPCR) superfamily. The receptors are seven-pass transmembrane proteins that respond to extracellular cues and activate intracellular signal transduction pathways. This protein was reported to be a receptor for lysophosphatidylcholine action, but PubMedID: 15653487 retracts this finding and instead suggests this protein to be an effector of lysophosphatidylcholine action. This protein may have proton-sensing activity and may be a receptor for oxidized free fatty acids. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

LOC124903398 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPR132	NM_013345.4	c.*1105G>A		3_prime_UTR_variant	4/4	ENST00000329797.8
LOC124903398	XR_007064368.1	n.335-5520C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPR132	ENST00000329797.8	c.*1105G>A		3_prime_UTR_variant	4/4	1	NM_013345.4	A2
GPR132	ENST00000392585.2	c.*1105G>A		3_prime_UTR_variant	3/3	1		P2
GPR132	ENST00000551869.1	c.*2274G>A		3_prime_UTR_variant, NMD_transcript_variant	3/3	1

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76979 AN: 152088 Hom.: 22267 Cov.: 34

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.543

GnomAD4 exome AF: 0.614 AC: 70 AN: 114 Hom.: 20 Cov.: 0 AF XY: 0.635 AC XY: 47 AN XY: 74

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.638

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.506 AC: 76989 AN: 152206 Hom.: 22264 Cov.: 34 AF XY: 0.505 AC XY: 37608 AN XY: 74406

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.543

Alfa AF: 0.537 Hom.: 3089

Bravo AF: 0.486

Asia WGS AF: 0.411 AC: 1429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.43

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: rs12890396; hg19: chr14-105516226; COSMIC: COSV61677739; COSMIC: COSV61677739;