rs2289912

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000373563.9(GIGYF2):​c.1378C>A​(p.Pro460Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0323 in 1,613,548 control chromosomes in the GnomAD database, including 2,427 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.033 ( 237 hom., cov: 32)
Exomes 𝑓: 0.032 ( 2190 hom. )

Consequence

GIGYF2
ENST00000373563.9 missense

Scores

2
15

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.66
Variant links:
Genes affected
GIGYF2 (HGNC:11960): (GRB10 interacting GYF protein 2) This gene contains CAG trinucleotide repeats and encodes a protein containing several stretches of polyglutamine residues. The encoded protein may be involved in the regulation of tyrosine kinase receptor signaling. This gene is located in a chromosomal region that was genetically linked to Parkinson disease type 11, and mutations in this gene were thought to be causative for this disease. However, more recent studies in different populations have been unable to replicate this association. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0011896789).
BP6
Variant 2-232794843-C-A is Benign according to our data. Variant chr2-232794843-C-A is described in ClinVar as [Benign]. Clinvar id is 1295070.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-232794843-C-A is described in Lovd as [Likely_benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GIGYF2NM_001103146.3 linkuse as main transcriptc.1378C>A p.Pro460Thr missense_variant 13/29 ENST00000373563.9 NP_001096616.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GIGYF2ENST00000373563.9 linkuse as main transcriptc.1378C>A p.Pro460Thr missense_variant 13/291 NM_001103146.3 ENSP00000362664 P4Q6Y7W6-1

Frequencies

GnomAD3 genomes
AF:
0.0330
AC:
5020
AN:
152108
Hom.:
237
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00697
Gnomad AMI
AF:
0.0560
Gnomad AMR
AF:
0.0489
Gnomad ASJ
AF:
0.0156
Gnomad EAS
AF:
0.231
Gnomad SAS
AF:
0.0861
Gnomad FIN
AF:
0.0760
Gnomad MID
AF:
0.0538
Gnomad NFE
AF:
0.0204
Gnomad OTH
AF:
0.0296
GnomAD3 exomes
AF:
0.0547
AC:
13736
AN:
251304
Hom.:
805
AF XY:
0.0540
AC XY:
7339
AN XY:
135804
show subpopulations
Gnomad AFR exome
AF:
0.00720
Gnomad AMR exome
AF:
0.0741
Gnomad ASJ exome
AF:
0.0179
Gnomad EAS exome
AF:
0.225
Gnomad SAS exome
AF:
0.0798
Gnomad FIN exome
AF:
0.0705
Gnomad NFE exome
AF:
0.0219
Gnomad OTH exome
AF:
0.0452
GnomAD4 exome
AF:
0.0323
AC:
47154
AN:
1461322
Hom.:
2190
Cov.:
31
AF XY:
0.0335
AC XY:
24324
AN XY:
727010
show subpopulations
Gnomad4 AFR exome
AF:
0.00678
Gnomad4 AMR exome
AF:
0.0704
Gnomad4 ASJ exome
AF:
0.0180
Gnomad4 EAS exome
AF:
0.251
Gnomad4 SAS exome
AF:
0.0787
Gnomad4 FIN exome
AF:
0.0711
Gnomad4 NFE exome
AF:
0.0183
Gnomad4 OTH exome
AF:
0.0351
GnomAD4 genome
AF:
0.0330
AC:
5021
AN:
152226
Hom.:
237
Cov.:
32
AF XY:
0.0374
AC XY:
2783
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.00700
Gnomad4 AMR
AF:
0.0492
Gnomad4 ASJ
AF:
0.0156
Gnomad4 EAS
AF:
0.230
Gnomad4 SAS
AF:
0.0862
Gnomad4 FIN
AF:
0.0760
Gnomad4 NFE
AF:
0.0204
Gnomad4 OTH
AF:
0.0284
Alfa
AF:
0.0238
Hom.:
175
Bravo
AF:
0.0310
TwinsUK
AF:
0.0181
AC:
67
ALSPAC
AF:
0.0184
AC:
71
ESP6500AA
AF:
0.00749
AC:
33
ESP6500EA
AF:
0.0198
AC:
170
ExAC
AF:
0.0524
AC:
6359
Asia WGS
AF:
0.133
AC:
462
AN:
3478
EpiCase
AF:
0.0204
EpiControl
AF:
0.0208

ClinVar

Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxJun 09, 2021- -
GIGYF2-related disorder Benign:1
Benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesJul 17, 2019This 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
0.061
BayesDel_addAF
Benign
-0.54
T
BayesDel_noAF
Benign
-0.41
CADD
Benign
19
DANN
Benign
0.91
DEOGEN2
Benign
0.10
.;T;.;T;T;.;.;T
Eigen
Benign
-0.16
Eigen_PC
Benign
-0.083
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Uncertain
0.88
D;.;.;D;D;D;D;D
MetaRNN
Benign
0.0012
T;T;T;T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationTaster
Benign
0.71
P;P;P;P;P;P;P
PrimateAI
Benign
0.33
T
PROVEAN
Benign
-1.2
.;N;N;N;N;N;N;N
REVEL
Benign
0.11
Sift
Benign
0.13
.;T;T;T;T;T;T;T
Sift4G
Benign
0.26
T;T;T;T;T;T;T;T
Polyphen
0.012
.;B;.;B;.;.;.;.
Vest4
0.14
MPC
0.56
ClinPred
0.011
T
GERP RS
3.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.043
gMVP
0.23

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs2289912; hg19: chr2-233659553; COSMIC: COSV65247241; COSMIC: COSV65247241; API