rs10885330
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NR_028134.1(GUCY2GP):n.2610G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 152,184 control chromosomes in the GnomAD database, including 14,046 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.42 ( 14036 hom., cov: 33)
Exomes 𝑓: 0.51 ( 10 hom. )
Consequence
GUCY2GP
NR_028134.1 non_coding_transcript_exon
NR_028134.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0320
Genes affected
GUCY2GP (HGNC:31863): (guanylate cyclase 2G, pseudogene) Predicted to enable guanylate cyclase activity. Predicted to be located in external side of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.27).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GUCY2GP | NR_028134.1 | n.2610G>T | non_coding_transcript_exon_variant | 16/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GUCY2GP | ENST00000479705.5 | n.2861G>T | non_coding_transcript_exon_variant | 18/21 | |||||
ENST00000638284.2 | n.1843G>T | non_coding_transcript_exon_variant | 14/17 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.420 AC: 63839AN: 151984Hom.: 14032 Cov.: 33
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GnomAD4 exome AF: 0.512 AC: 42AN: 82Hom.: 10 Cov.: 0 AF XY: 0.500 AC XY: 29AN XY: 58
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GnomAD4 genome ? AF: 0.420 AC: 63884AN: 152102Hom.: 14036 Cov.: 33 AF XY: 0.423 AC XY: 31453AN XY: 74356
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ClinVar
Not reported inComputational scores
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Name
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Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at