17-8014859-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_000180.4(GUCY2D):c.2577G>A(p.Pro859Pro) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000180.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GUCY2D | NM_000180.4 | c.2577G>A | p.Pro859Pro | splice_region_variant, synonymous_variant | Exon 14 of 20 | ENST00000254854.5 | NP_000171.1 | |
GUCY2D | XM_011523816.2 | c.2577G>A | p.Pro859Pro | splice_region_variant, synonymous_variant | Exon 13 of 19 | XP_011522118.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GUCY2D | ENST00000254854.5 | c.2577G>A | p.Pro859Pro | splice_region_variant, synonymous_variant | Exon 14 of 20 | 1 | NM_000180.4 | ENSP00000254854.4 | ||
ENSG00000279174 | ENST00000623126.1 | n.1520C>T | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251356Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135872
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461856Hom.: 0 Cov.: 35 AF XY: 0.00000275 AC XY: 2AN XY: 727228
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at