2-232747646-A-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001103146.3(GIGYF2):āc.73A>Gā(p.Thr25Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000148 in 1,613,684 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001103146.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000481 AC: 121AN: 251318Hom.: 1 AF XY: 0.000486 AC XY: 66AN XY: 135826
GnomAD4 exome AF: 0.000139 AC: 203AN: 1461364Hom.: 0 Cov.: 31 AF XY: 0.000144 AC XY: 105AN XY: 727030
GnomAD4 genome AF: 0.000236 AC: 36AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74498
ClinVar
Submissions by phenotype
GIGYF2-related disorder Benign:1
This variant is classified as likely 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