rs275737

chr15-39886812-C-T

Variant summary

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

The NM_007223.3(GPR176):c.172+33043G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0884 in 152,186 control chromosomes in the GnomAD database, including 982 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 0.088 (982 hom., cov: 32)
• Consequence: GPR176 NM_007223.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422

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=-0.62).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPR176	NM_007223.3	c.172+33043G>A		intron_variant		ENST00000561100.2
GPR176	NM_001271854.2	c.172+33043G>A		intron_variant
GPR176	XM_017021878.3	c.-65+33043G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPR176	ENST00000561100.2	c.172+33043G>A		intron_variant		1	NM_007223.3	P1
GPR176	ENST00000299092.4	c.172+33043G>A		intron_variant		1
GPR176	ENST00000558041.5	n.98-25890G>A		intron_variant, non_coding_transcript_variant		3
GPR176	ENST00000560729.1	n.72+7644G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0883 AC: 13425 AN: 152066 Hom.: 970 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.0182

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.0594

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0417

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.0884 AC: 13458 AN: 152186 Hom.: 982 Cov.: 32 AF XY: 0.0940 AC XY: 6993 AN XY: 74392

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.0182

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.0599

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.0417

Gnomad4 OTH AF: 0.0847

Alfa AF: 0.0588 Hom.: 564

Bravo AF: 0.0987

Asia WGS AF: 0.166 AC: 576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
Cadd	Benign	12
Dann	Benign	0.79

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: rs275737; hg19: chr15-40179013;