chr5-74721765-G-C
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP3BP4_StrongBP6_Very_StrongBS1BS2
The NM_032380.5(GFM2):āc.2230C>Gā(p.Arg744Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0175 in 1,612,260 control chromosomes in the GnomAD database, including 273 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R744Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_032380.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GFM2 | NM_032380.5 | c.2230C>G | p.Arg744Gly | missense_variant | 21/21 | ENST00000296805.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GFM2 | ENST00000296805.8 | c.2230C>G | p.Arg744Gly | missense_variant | 21/21 | 1 | NM_032380.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0146 AC: 2219AN: 152102Hom.: 13 Cov.: 32
GnomAD3 exomes AF: 0.0166 AC: 4140AN: 249612Hom.: 40 AF XY: 0.0160 AC XY: 2155AN XY: 134846
GnomAD4 exome AF: 0.0178 AC: 26015AN: 1460040Hom.: 260 Cov.: 30 AF XY: 0.0176 AC XY: 12773AN XY: 726300
GnomAD4 genome AF: 0.0146 AC: 2222AN: 152220Hom.: 13 Cov.: 32 AF XY: 0.0138 AC XY: 1024AN XY: 74416
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 09, 2013 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
GFM2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 23, 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at