rs952193754
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM4PP3PP5_Moderate
The NM_000180.4(GUCY2D):βc.238_252delβ(p.Ala80_Leu84del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000734 in 1,498,798 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (β ). Synonymous variant affecting the same amino acid position (i.e. A76A) has been classified as Likely benign.
Frequency
Consequence
NM_000180.4 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GUCY2D | NM_000180.4 | c.238_252del | p.Ala80_Leu84del | inframe_deletion | 2/20 | ENST00000254854.5 | |
GUCY2D | XM_011523816.2 | c.238_252del | p.Ala80_Leu84del | inframe_deletion | 1/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GUCY2D | ENST00000254854.5 | c.238_252del | p.Ala80_Leu84del | inframe_deletion | 2/20 | 1 | NM_000180.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000213 AC: 2AN: 93704Hom.: 0 AF XY: 0.0000189 AC XY: 1AN XY: 52908
GnomAD4 exome AF: 0.00000594 AC: 8AN: 1346668Hom.: 0 AF XY: 0.00000753 AC XY: 5AN XY: 663880
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74300
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jan 22, 2021 | - - |
Cone dystrophy Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | NIHR Bioresource Rare Diseases, University of Cambridge | Jan 01, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at