rs1202874

Variant names:

• chrX-151179756-C-G
• rs1202874
• NM_004224.3:c.188-15C>G

Your query was ambiguous. Multiple possible variants found:

• chrX-151179756-C-G
• chrX-151179756-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_004224.3(GPR50):​c.188-15C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 22)
  • Exomes 𝑓: 9.9e-7 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: GPR50 NM_004224.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 12 publications found

Genes affected

GPR50 (HGNC:4506): (G protein-coupled receptor 50) This gene product belongs to the G-protein coupled receptor 1 family. Even though this protein shares similarity with the melatonin receptors, it does not bind melatonin, however, it inhibits melatonin receptor 1A function through heterodimerization. Polymorphic variants of this gene have been associated with bipolar affective disorder in women. [provided by RefSeq, Jan 2010]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR50	NM_004224.3	c.188-15C>G		intron_variant	Intron 1 of 1	ENST00000218316.4	NP_004215.2
GPR50	XM_011531216.3	c.-336C>G		upstream_gene_variant			XP_011529518.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR50	ENST00000218316.4	c.188-15C>G		intron_variant	Intron 1 of 1	1	NM_004224.3	ENSP00000218316.3

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD2 exomes AF: 0.00000698 AC: 1 AN: 143339 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000804

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 9.89e-7 AC: 1 AN: 1011301 Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0 AN XY: 307557

African (AFR) AF: 0.00 AC: 0 AN: 24128

American (AMR) AF: 0.00 AC: 0 AN: 28982

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15964

East Asian (EAS) AF: 0.0000338 AC: 1 AN: 29572

South Asian (SAS) AF: 0.00 AC: 0 AN: 45418

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38445

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3807

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 782317

Other (OTH) AF: 0.00 AC: 0 AN: 42668

GnomAD4 genome Cov.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.90
DANN	Benign	0.63
PhyloP100		-1.1

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: rs1202874; hg19: chrX-150348228;