GeneBe

rs759525243

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001103146.3(GIGYF2):​c.268-19_268-6delTTTTTTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000164 in 607,962 control chromosomes in the GnomAD database, including 1 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.000016 ( 1 hom. )

Consequence

GIGYF2
NM_001103146.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.60

Publications

0 publications found
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]
GIGYF2 Gene-Disease associations (from GenCC):
  • Parkinson disease 11, autosomal dominant, susceptibility to
    Inheritance: AD, Unknown Classification: MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Genomics England PanelApp

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2
High AC in GnomAdExome4 at 10 AD,Unknown gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GIGYF2NM_001103146.3 linkc.268-19_268-6delTTTTTTTTTTTTTT splice_region_variant, intron_variant Intron 5 of 28 ENST00000373563.9 NP_001096616.1 Q6Y7W6-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GIGYF2ENST00000373563.9 linkc.268-25_268-12delTTTTTTTTTTTTTT intron_variant Intron 5 of 28 1 NM_001103146.3 ENSP00000362664.5 Q6Y7W6-1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.0000164
AC:
10
AN:
607962
Hom.:
1
AF XY:
0.00000931
AC XY:
3
AN XY:
322394
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
14868
American (AMR)
AF:
0.00
AC:
0
AN:
25780
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
16078
East Asian (EAS)
AF:
0.00
AC:
0
AN:
31438
South Asian (SAS)
AF:
0.00
AC:
0
AN:
48302
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
37014
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2268
European-Non Finnish (NFE)
AF:
0.0000199
AC:
8
AN:
402476
Other (OTH)
AF:
0.0000673
AC:
2
AN:
29738
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.719
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs759525243; hg19: chr2-233620907; API