chr15-39886812-C-T

Variant names:

• chr15-39886812-C-T
• rs275737
• NM_007223.3:c.172+33043G>A

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+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
• 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=-0.62).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.204 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+33043G>A		intron	N/A	NP_009154.1	Q14439-1
	GPR176	NM_001271854.2		c.172+33043G>A		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+33043G>A		intron	N/A	ENSP00000453076.1	Q14439-1
	GPR176	ENST00000299092.4	TSL:1	c.172+33043G>A		intron	N/A	ENSP00000299092.3	Q14439-3
	GPR176	ENST00000558041.5	TSL:3	n.98-25890G>A		intron	N/A

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

African (AFR) AF: 0.108 AC: 4466 AN: 41526

American (AMR) AF: 0.210 AC: 3215 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0182 AC: 63 AN: 3470

East Asian (EAS) AF: 0.176 AC: 912 AN: 5180

South Asian (SAS) AF: 0.0599 AC: 289 AN: 4824

European-Finnish (FIN) AF: 0.138 AC: 1464 AN: 10578

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0417 AC: 2835 AN: 67998

Other (OTH) AF: 0.0847 AC: 179 AN: 2114

Alfa AF: 0.0645 Hom.: 840

Bravo AF: 0.0987

Asia WGS AF: 0.166 AC: 576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		0.42
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: rs275737; hg19: chr15-40179013;