rs275715

Variant names:

• chr15-39820118-G-A
• rs275715
• NM_007223.3:c.173-12860C>T

Variant summary

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

The NM_007223.3(GPR176):​c.173-12860C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0945 in 152,196 control chromosomes in the GnomAD database, including 1,880 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 0.094 (1880 hom., cov: 32)
• Consequence: GPR176 NM_007223.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160

Genes affected

GPR176 (HGNC:32370): (G protein-coupled receptor 176) Members of the G protein-coupled receptor family, such as GPR176, are cell surface receptors involved in responses to hormones, growth factors, and neurotransmitters (Hata et al., 1995 [PubMed 7893747]).[supplied by OMIM, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR176	NM_007223.3	c.173-12860C>T		intron_variant	Intron 1 of 2	ENST00000561100.2	NP_009154.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR176	ENST00000561100.2	c.173-12860C>T		intron_variant	Intron 1 of 2	1	NM_007223.3	ENSP00000453076.1

Frequencies

GnomAD3 genomes AF: 0.0942 AC: 14330 AN: 152078 Hom.: 1867 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0389

Gnomad ASJ AF: 0.0253

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.0157

Gnomad FIN AF: 0.0284

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0135

Gnomad OTH AF: 0.0733

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

GnomAD4 genome AF: 0.0945 AC: 14378 AN: 152196 Hom.: 1880 Cov.: 32 AF XY: 0.0913 AC XY: 6798 AN XY: 74426

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.0388

Gnomad4 ASJ AF: 0.0253

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.0158

Gnomad4 FIN AF: 0.0284

Gnomad4 NFE AF: 0.0135

Gnomad4 OTH AF: 0.0725

Alfa AF: 0.0362 Hom.: 260

Bravo AF: 0.106

Asia WGS AF: 0.0340 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.6
DANN	Benign	0.78

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: rs275715; hg19: chr15-40112319;