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
Consequence
ENST00000373563.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GIGYF2 | NM_001103146.3 | c.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 |
---|---|---|---|---|---|---|---|---|---|---|
GIGYF2 | ENST00000373563.9 | c.1378C>A | p.Pro460Thr | missense_variant | 13/29 | 1 | NM_001103146.3 | ENSP00000362664 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0330 AC: 5020AN: 152108Hom.: 237 Cov.: 32
GnomAD3 exomes AF: 0.0547 AC: 13736AN: 251304Hom.: 805 AF XY: 0.0540 AC XY: 7339AN XY: 135804
GnomAD4 exome AF: 0.0323 AC: 47154AN: 1461322Hom.: 2190 Cov.: 31 AF XY: 0.0335 AC XY: 24324AN XY: 727010
GnomAD4 genome AF: 0.0330 AC: 5021AN: 152226Hom.: 237 Cov.: 32 AF XY: 0.0374 AC XY: 2783AN XY: 74402
ClinVar
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 | Jun 09, 2021 | - - |
GIGYF2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 17, 2019 | 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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at