15-39889478-T-C

Variant names:

• chr15-39889478-T-C
• rs386220
• NM_007223.3:c.172+30377A>G

Variant summary

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

The NM_007223.3(GPR176):​c.172+30377A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.99 in 151,900 control chromosomes in the GnomAD database, including 74,516 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 0.99 (74516 hom., cov: 29)
• Consequence: GPR176 NM_007223.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 3 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007223.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR176	NM_007223.3	MANE Select	c.172+30377A>G		intron	N/A	NP_009154.1	Q14439-1
	GPR176	NM_001271854.2		c.172+30377A>G		intron	N/A	NP_001258783.1	Q14439-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR176	ENST00000561100.2	TSL:1 MANE Select	c.172+30377A>G		intron	N/A	ENSP00000453076.1	Q14439-1
	GPR176	ENST00000299092.4	TSL:1	c.172+30377A>G		intron	N/A	ENSP00000299092.3	Q14439-3
	GPR176	ENST00000558041.5	TSL:3	n.98-28556A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.990 AC: 150337 AN: 151782 Hom.: 74457 Cov.: 29

Gnomad AFR AF: 0.997

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.988

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.997

Gnomad FIN AF: 0.983

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.991

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

GnomAD4 genome AF: 0.990 AC: 150455 AN: 151900 Hom.: 74516 Cov.: 29 AF XY: 0.991 AC XY: 73551 AN XY: 74240

African (AFR) AF: 0.997 AC: 41189 AN: 41314

American (AMR) AF: 0.988 AC: 15079 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3428 AN: 3468

East Asian (EAS) AF: 1.00 AC: 5182 AN: 5182

South Asian (SAS) AF: 0.997 AC: 4799 AN: 4814

European-Finnish (FIN) AF: 0.983 AC: 10364 AN: 10546

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 0.988 AC: 67168 AN: 68016

Other (OTH) AF: 0.991 AC: 2073 AN: 2092

Alfa AF: 0.989 Hom.: 8657

Bravo AF: 0.991

Asia WGS AF: 0.999 AC: 3433 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.51
PhyloP100		0.077
Mutation Taster		=100/0	polymorphism (auto)

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: rs386220; hg19: chr15-40181679;