NM_014373.3:c.64C>A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

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. 13/20 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

Scores

1
17

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.0410
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GPR160NM_014373.3 linkc.64C>A p.Leu22Ile missense_variant Exon 4 of 4 ENST00000355897.10 NP_055188.1 Q9UJ42

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GPR160ENST00000355897.10 linkc.64C>A p.Leu22Ile missense_variant Exon 4 of 4 1 NM_014373.3 ENSP00000348161.5 Q9UJ42

Frequencies

GnomAD3 genomes
AF:
0.000618
AC:
94
AN:
152156
Hom.:
2
Cov.:
32
show subpopulations
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
GnomAD3 exomes
AF:
0.00171
AC:
384
AN:
225036
Hom.:
6
AF XY:
0.00243
AC XY:
296
AN XY:
121758
show subpopulations
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 SAS exome
AF:
0.0155
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
show subpopulations
Gnomad4 AFR exome
AF:
0.0000316
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0145
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000365
Gnomad4 OTH exome
AF:
0.000815
GnomAD4 genome
AF:
0.000624
AC:
95
AN:
152274
Hom.:
2
Cov.:
32
AF XY:
0.000873
AC XY:
65
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.0000481
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.0191
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000831
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

Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

GPR160-related disorder Benign:1
May 28, 2019
PreventionGenetics, part of Exact Sciences
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

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;T;T;T;T
MetaRNN
Benign
0.0040
T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.4
M;.;.;.;.
PrimateAI
Benign
0.31
T
PROVEAN
Benign
-1.1
N;N;N;N;N
REVEL
Benign
0.018
Sift
Benign
0.12
T;D;T;T;T
Sift4G
Benign
0.34
T;D;T;D;T
Polyphen
0.70
P;.;.;.;.
Vest4
0.33
MutPred
0.28
Gain of catalytic residue at L27 (P = 0.0705);Gain of catalytic residue at L27 (P = 0.0705);Gain of catalytic residue at L27 (P = 0.0705);Gain of catalytic residue at L27 (P = 0.0705);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

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs200182513; hg19: chr3-169801824; API