2-232735194-A-C
Position:
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_001103146.3(GIGYF2):c.-4A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 1,591,010 control chromosomes in the GnomAD database, including 105,819 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.32 ( 7997 hom., cov: 32)
Exomes 𝑓: 0.36 ( 97822 hom. )
Consequence
GIGYF2
NM_001103146.3 5_prime_UTR
NM_001103146.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.72
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.23).
BP6
Variant 2-232735194-A-C is Benign according to our data. Variant chr2-232735194-A-C is described in ClinVar as [Benign]. Clinvar id is 1246966.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-232735194-A-C is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GIGYF2 | NM_001103146.3 | c.-4A>C | 5_prime_UTR_variant | 3/29 | ENST00000373563.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GIGYF2 | ENST00000373563.9 | c.-4A>C | 5_prime_UTR_variant | 3/29 | 1 | NM_001103146.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.317 AC: 48158AN: 152008Hom.: 7988 Cov.: 32
GnomAD3 genomes
AF:
AC:
48158
AN:
152008
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.349 AC: 87432AN: 250634Hom.: 16996 AF XY: 0.367 AC XY: 49758AN XY: 135454
GnomAD3 exomes
AF:
AC:
87432
AN:
250634
Hom.:
AF XY:
AC XY:
49758
AN XY:
135454
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.358 AC: 515414AN: 1438884Hom.: 97822 Cov.: 27 AF XY: 0.367 AC XY: 263075AN XY: 717100
GnomAD4 exome
AF:
AC:
515414
AN:
1438884
Hom.:
Cov.:
27
AF XY:
AC XY:
263075
AN XY:
717100
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.317 AC: 48182AN: 152126Hom.: 7997 Cov.: 32 AF XY: 0.316 AC XY: 23515AN XY: 74386
GnomAD4 genome
AF:
AC:
48182
AN:
152126
Hom.:
Cov.:
32
AF XY:
AC XY:
23515
AN XY:
74386
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1716
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 22, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at