17-8014859-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000180.4(GUCY2D):c.2577G>T(p.Pro859=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00382 in 1,614,102 control chromosomes in the GnomAD database, including 141 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000180.4 splice_region, synonymous
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 | UniProt |
---|---|---|---|---|---|---|---|
GUCY2D | NM_000180.4 | c.2577G>T | p.Pro859= | splice_region_variant, synonymous_variant | 14/20 | ENST00000254854.5 | |
GUCY2D | XM_011523816.2 | c.2577G>T | p.Pro859= | splice_region_variant, synonymous_variant | 13/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GUCY2D | ENST00000254854.5 | c.2577G>T | p.Pro859= | splice_region_variant, synonymous_variant | 14/20 | 1 | NM_000180.4 | P1 | |
ENST00000623126.1 | n.1520C>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.00581 AC: 884AN: 152132Hom.: 13 Cov.: 32
GnomAD3 exomes AF: 0.00679 AC: 1707AN: 251356Hom.: 45 AF XY: 0.00834 AC XY: 1133AN XY: 135872
GnomAD4 exome AF: 0.00360 AC: 5265AN: 1461852Hom.: 127 Cov.: 35 AF XY: 0.00470 AC XY: 3420AN XY: 727228
GnomAD4 genome AF: 0.00587 AC: 893AN: 152250Hom.: 14 Cov.: 32 AF XY: 0.00629 AC XY: 468AN XY: 74446
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Apr 28, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 13, 2015 | - - |
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 - |
Cone-rod dystrophy 6;C2931258:Leber congenital amaurosis 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at