rs140638938
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_000180.4(GUCY2D):c.1315G>A(p.Gly439Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000178 in 1,612,710 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G439W) has been classified as Uncertain significance.
Frequency
Consequence
NM_000180.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GUCY2D | NM_000180.4 | c.1315G>A | p.Gly439Arg | missense_variant | 4/20 | ENST00000254854.5 | |
GUCY2D | XM_011523816.2 | c.1315G>A | p.Gly439Arg | missense_variant | 3/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GUCY2D | ENST00000254854.5 | c.1315G>A | p.Gly439Arg | missense_variant | 4/20 | 1 | NM_000180.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152218Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000369 AC: 90AN: 244094Hom.: 1 AF XY: 0.000513 AC XY: 68AN XY: 132550
GnomAD4 exome AF: 0.000182 AC: 266AN: 1460374Hom.: 3 Cov.: 33 AF XY: 0.000286 AC XY: 208AN XY: 726320
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152336Hom.: 1 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74490
ClinVar
Submissions by phenotype
Choroidal dystrophy, central areolar, 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jan 01, 2016 | This variant was classified as: Uncertain significance. This variant was inherited from a parent. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 31, 2016 | - - |
Nystagmus;C0476397:Abnormal electroretinogram Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jul 11, 2014 | - - |
Cone-rod dystrophy 6;C2931258:Leber congenital amaurosis 1 Benign:1
Likely 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