rs371622656
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 8P and 16B. PVS1BP6_Very_StrongBA1
The NM_001103146.3(GIGYF2):c.3629_3630insGC(p.Gln1211fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0371 in 1,385,702 control chromosomes in the GnomAD database, including 2,014 homozygotes. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P1210P) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001103146.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GIGYF2 | NM_001103146.3 | c.3629_3630insGC | p.Gln1211fs | frameshift_variant | 27/29 | ENST00000373563.9 | NP_001096616.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GIGYF2 | ENST00000373563.9 | c.3629_3630insGC | p.Gln1211fs | frameshift_variant | 27/29 | 1 | NM_001103146.3 | ENSP00000362664.5 |
Frequencies
GnomAD3 genomes AF: 0.0577 AC: 5016AN: 86914Hom.: 236 Cov.: 30
GnomAD3 exomes AF: 0.0464 AC: 7524AN: 162200Hom.: 326 AF XY: 0.0455 AC XY: 4133AN XY: 90768
GnomAD4 exome AF: 0.0357 AC: 46337AN: 1298714Hom.: 1778 Cov.: 61 AF XY: 0.0369 AC XY: 23920AN XY: 647452
GnomAD4 genome AF: 0.0577 AC: 5016AN: 86988Hom.: 236 Cov.: 30 AF XY: 0.0655 AC XY: 2791AN XY: 42634
ClinVar
Submissions by phenotype
Parkinson disease 11, autosomal dominant, susceptibility to Benign:2
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | Apr 22, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Mar 26, 2015 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: 23.92% East Asian, with 176 homozygotes (VQSRTrancheINDEL99.00to99.50) - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at