15-39865113-G-A

Variant names:

• chr15-39865113-G-A
• rs2117975
• NM_007223.3:c.172+54742C>T

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+54742C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,070 control chromosomes in the GnomAD database, including 1,188 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 0.12 (1188 hom., cov: 32)
• Consequence: GPR176 NM_007223.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 5 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR176	NM_007223.3	c.172+54742C>T		intron_variant	Intron 1 of 2	ENST00000561100.2	NP_009154.1
GPR176	NM_001271854.2	c.172+54742C>T		intron_variant	Intron 1 of 3		NP_001258783.1
GPR176	XM_017021878.3	c.-65+54742C>T		intron_variant	Intron 1 of 1		XP_016877367.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR176	ENST00000561100.2	c.172+54742C>T		intron_variant	Intron 1 of 2	1	NM_007223.3	ENSP00000453076.1
GPR176	ENST00000299092.4	c.172+54742C>T		intron_variant	Intron 1 of 3	1		ENSP00000299092.3
GPR176	ENST00000558041.5	n.98-4191C>T		intron_variant	Intron 1 of 2	3
GPR176	ENST00000560729.1	n.73-2694C>T		intron_variant	Intron 1 of 5	3

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18126 AN: 151952 Hom.: 1192 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0519

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0708

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.119 AC: 18133 AN: 152070 Hom.: 1188 Cov.: 32 AF XY: 0.117 AC XY: 8673 AN XY: 74356

African (AFR) AF: 0.141 AC: 5843 AN: 41490

American (AMR) AF: 0.122 AC: 1868 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3466

East Asian (EAS) AF: 0.0518 AC: 269 AN: 5192

South Asian (SAS) AF: 0.111 AC: 535 AN: 4820

European-Finnish (FIN) AF: 0.0708 AC: 749 AN: 10572

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7746 AN: 67932

Other (OTH) AF: 0.140 AC: 297 AN: 2114

Alfa AF: 0.119 Hom.: 1432

Bravo AF: 0.124

Asia WGS AF: 0.116 AC: 402 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.34
DANN	Benign	0.16
PhyloP100		-1.5
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: rs2117975; hg19: chr15-40157314;