rs737575
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_003923.2(GUCY1B2):n.377-1045T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0428 in 152,260 control chromosomes in the GnomAD database, including 267 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 0.043 ( 267 hom., cov: 33)
Consequence
GUCY1B2
NR_003923.2 intron, non_coding_transcript
NR_003923.2 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.38
Genes affected
GUCY1B2 (HGNC:4686): (guanylate cyclase 1 soluble subunit beta 2 (pseudogene)) Predicted to enable several functions, including GTP binding activity; guanylate cyclase activity; and heme binding activity. Predicted to be involved in cGMP-mediated signaling. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GUCY1B2 | NR_003923.2 | n.377-1045T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GUCY1B2 | ENST00000531898.5 | n.170-1045T>C | intron_variant, non_coding_transcript_variant | ||||||
GUCY1B2 | ENST00000533288.5 | n.155+27617T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0426 AC: 6484AN: 152142Hom.: 257 Cov.: 33
GnomAD3 genomes
?
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AC:
6484
AN:
152142
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Cov.:
33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0428 AC: 6515AN: 152260Hom.: 267 Cov.: 33 AF XY: 0.0473 AC XY: 3518AN XY: 74436
GnomAD4 genome
?
AF:
AC:
6515
AN:
152260
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Cov.:
33
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3518
AN XY:
74436
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Asia WGS
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AC:
349
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at