ENST00000817155.1:n.19C>T

Variant names:

• chr1-27392450-G-A
• rs2504785
• ENST00000817155.1:n.19C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000817155.1(ENSG00000306354):​n.19C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.881 in 152,250 control chromosomes in the GnomAD database, including 59,371 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 0.88 (59371 hom., cov: 33)
• Consequence: ENSG00000306354 ENST00000817155.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793
• Publications: 3 publications found

Genes affected

ENSG00000306354 (HGNC:):

GPR3 (HGNC:4484): (G protein-coupled receptor 3) This gene is a member of the G protein-coupled receptor family and is found in the cell membrane. G protein-coupled receptors, characterized by a seven transmembrane domain motif, are involved in translating outside signals into G protein mediated intracellular effects. The encoded protein activates adenylate cyclase and modulates amyloid-beta production in a mouse model, suggesting that it may play a role in Alzheimer's disease. [provided by RefSeq, Oct 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR3	NM_005281.4	c.-293G>A		upstream_gene_variant		ENST00000374024.4	NP_005272.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR3	ENST00000374024.4	c.-293G>A		upstream_gene_variant		1	NM_005281.4	ENSP00000363136.3

Frequencies

GnomAD3 genomes AF: 0.881 AC: 134043 AN: 152132 Hom.: 59332 Cov.: 33

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.881 AC: 134135 AN: 152250 Hom.: 59371 Cov.: 33 AF XY: 0.884 AC XY: 65831 AN XY: 74430

African (AFR) AF: 0.785 AC: 32637 AN: 41554

American (AMR) AF: 0.930 AC: 14226 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 3123 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5156 AN: 5162

South Asian (SAS) AF: 0.961 AC: 4642 AN: 4830

European-Finnish (FIN) AF: 0.906 AC: 9617 AN: 10614

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.908 AC: 61722 AN: 67998

Other (OTH) AF: 0.889 AC: 1879 AN: 2114

Alfa AF: 0.894 Hom.: 3228

Bravo AF: 0.895

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.0
PhyloP100		-0.79
PromoterAI		-0.10	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2504785; hg19: chr1-27718954;