chr5-74721782-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 3P and 5B. PM2PP3BP6BS1
The NM_032380.5(GFM2):c.2213G>A(p.Gly738Asp) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000144 in 1,601,912 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_032380.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GFM2 | NM_032380.5 | c.2213G>A | p.Gly738Asp | missense_variant, splice_region_variant | 21/21 | ENST00000296805.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GFM2 | ENST00000296805.8 | c.2213G>A | p.Gly738Asp | missense_variant, splice_region_variant | 21/21 | 1 | NM_032380.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000318 AC: 76AN: 239350Hom.: 0 AF XY: 0.000286 AC XY: 37AN XY: 129214
GnomAD4 exome AF: 0.000147 AC: 213AN: 1449662Hom.: 1 Cov.: 30 AF XY: 0.000153 AC XY: 110AN XY: 720814
GnomAD4 genome AF: 0.000112 AC: 17AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74426
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2022 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Oct 18, 2021 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at