rs34598902
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000180.4(GUCY2D):c.2101C>T(p.Pro701Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0338 in 1,613,188 control chromosomes in the GnomAD database, including 2,099 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000180.4 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 |
---|---|---|---|---|---|---|---|---|
GUCY2D | NM_000180.4 | c.2101C>T | p.Pro701Ser | missense_variant | 10/20 | ENST00000254854.5 | NP_000171.1 | |
GUCY2D | XM_011523816.2 | c.2101C>T | p.Pro701Ser | missense_variant | 9/19 | XP_011522118.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GUCY2D | ENST00000254854.5 | c.2101C>T | p.Pro701Ser | missense_variant | 10/20 | 1 | NM_000180.4 | ENSP00000254854.4 |
Frequencies
GnomAD3 genomes AF: 0.0395 AC: 6004AN: 152180Hom.: 254 Cov.: 32
GnomAD3 exomes AF: 0.0527 AC: 13104AN: 248670Hom.: 683 AF XY: 0.0526 AC XY: 7088AN XY: 134724
GnomAD4 exome AF: 0.0332 AC: 48458AN: 1460890Hom.: 1844 Cov.: 33 AF XY: 0.0346 AC XY: 25146AN XY: 726712
GnomAD4 genome AF: 0.0395 AC: 6012AN: 152298Hom.: 255 Cov.: 32 AF XY: 0.0434 AC XY: 3236AN XY: 74480
ClinVar
Submissions by phenotype
not provided Benign:4Other:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 29, 2023 | - - |
not provided, no classification provided | literature only | Retina International | - | - - |
Likely benign, no assertion criteria provided | literature only | Department of Ophthalmology and Visual Sciences Kyoto University | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | This variant is associated with the following publications: (PMID: 27884173, 11035546, 23424971, 20981092, 18055820, 15111605) - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in 1000Genomes: 180/2178=8.2% - |
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 03, 2014 | - - |
Leber congenital amaurosis 1 Benign:1
Likely benign, no assertion criteria provided | research | Laboratory of Genetics in Ophthalmology, Institut Imagine | - | - - |
Cone-rod dystrophy 6;C2931258:Leber congenital amaurosis 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Cone-rod dystrophy 6;C2931258:Leber congenital amaurosis 1;C4551884:Choroidal dystrophy, central areolar, 1;C5231408:Night blindness, congenital stationary, type1i Benign:1
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Sep 01, 2021 | - - |
Retinal dystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg | Jan 01, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at