rs200182513

Variant names:

• chr3-170084036-C-A
• rs200182513
• NM_014373.3:c.64C>A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6 BS1 BS2

The NM_014373.3(GPR160):​c.64C>A​(p.Leu22Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000832 in 1,578,902 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.00062 (2 hom., cov: 32)
  • Exomes 𝑓: 0.00085 (19 hom.)
• Consequence: GPR160 NM_014373.3 missense
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.0410
• Publications: 0 publications found

Genes affected

GPR160 (HGNC:23693): (G protein-coupled receptor 160) Predicted to enable G protein-coupled receptor activity. Predicted to be involved in G protein-coupled receptor signaling pathway. Located in plasma membrane. Part of receptor complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0040305555).
• BP6: Variant 3-170084036-C-A is Benign according to our data. Variant chr3-170084036-C-A is described in ClinVar as Benign. ClinVar VariationId is 3038858.Status of the report is no_assertion_criteria_provided, 0 stars.
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.000624 (95/152274) while in subpopulation SAS AF = 0.0191 (92/4828). AF 95% confidence interval is 0.0159. There are 2 homozygotes in GnomAd4. There are 65 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014373.3. 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
	GPR160	NM_014373.3	MANE Select	c.64C>A	p.Leu22Ile	missense	Exon 4 of 4	NP_055188.1	Q9UJ42

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR160	ENST00000355897.10	TSL:1 MANE Select	c.64C>A	p.Leu22Ile	missense	Exon 4 of 4	ENSP00000348161.5	Q9UJ42
	GPR160	ENST00000492492.5	TSL:1	c.64C>A	p.Leu22Ile	missense	Exon 5 of 5	ENSP00000418531.1	C9J0J1
	GPR160	ENST00000900470.1		c.64C>A	p.Leu22Ile	missense	Exon 4 of 4	ENSP00000570529.1

Frequencies

GnomAD3 genomes AF: 0.000618 AC: 94 AN: 152156 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.0000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0188

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.00171 AC: 384 AN: 225036 AF XY: 0.00243

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000950

Gnomad OTH exome AF: 0.000187

GnomAD4 exome AF: 0.000854 AC: 1218 AN: 1426628 Hom.: 19 Cov.: 27 AF XY: 0.00124 AC XY: 882 AN XY: 709148

African (AFR) AF: 0.0000316 AC: 1 AN: 31694

American (AMR) AF: 0.00 AC: 0 AN: 37794

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24508

East Asian (EAS) AF: 0.00 AC: 0 AN: 39300

South Asian (SAS) AF: 0.0145 AC: 1161 AN: 79886

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52524

Middle Eastern (MID) AF: 0.000714 AC: 4 AN: 5602

European-Non Finnish (NFE) AF: 0.00000365 AC: 4 AN: 1096458

Other (OTH) AF: 0.000815 AC: 48 AN: 58862

GnomAD4 genome AF: 0.000624 AC: 95 AN: 152274 Hom.: 2 Cov.: 32 AF XY: 0.000873 AC XY: 65 AN XY: 74446

African (AFR) AF: 0.0000481 AC: 2 AN: 41538

American (AMR) AF: 0.00 AC: 0 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5192

South Asian (SAS) AF: 0.0191 AC: 92 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10604

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68026

Other (OTH) AF: 0.00 AC: 0 AN: 2112

Alfa AF: 0.0000517 Hom.: 0

Bravo AF: 0.0000945

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000259 AC: 1

ExAC AF: 0.00196 AC: 238

Asia WGS AF: 0.00549 AC: 19 AN: 3474

ClinVar

ClinVar submissions

Significance: Benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	GPR160-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.083
BayesDel_addAF	Benign	-0.55	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	10
DANN	Benign	0.95
DEOGEN2	Benign	0.096	T
Eigen	Benign	-0.42
Eigen_PC	Benign	-0.54
FATHMM_MKL	Benign	0.16	N
LIST_S2	Benign	0.56	T
MetaRNN	Benign	0.0040	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.4	M
PhyloP100		0.041
PrimateAI	Benign	0.31	T
PROVEAN	Benign	-1.1	N
REVEL	Benign	0.018
Sift	Benign	0.12	T
Sift4G	Benign	0.34	T
Polyphen		0.70	P
Vest4		0.33
MutPred		0.28		Gain of catalytic residue at L27 (P = 0.0705)
MVP		0.014
MPC		0.23
ClinPred		0.024	T
GERP RS		2.5
Varity_R		0.082
gMVP		0.054
Mutation Taster		=98/2	polymorphism

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: rs200182513; hg19: chr3-169801824;