rs3217210
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_004963.4(GUCY2C):c.2158-8del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00080 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00088 ( 4 hom. )
Consequence
GUCY2C
NM_004963.4 splice_region, splice_polypyrimidine_tract, intron
NM_004963.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.995
Genes affected
GUCY2C (HGNC:4688): (guanylate cyclase 2C) This gene encodes a transmembrane protein that functions as a receptor for endogenous peptides guanylin and uroguanylin, and the heat-stable E. coli enterotoxin. The encoded protein activates the cystic fibrosis transmembrane conductance regulator. Mutations in this gene are associated with familial diarrhea (autosomal dominant) and meconium ileus (autosomal recessive). [provided by RefSeq, Nov 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant 12-14628744-GA-G is Benign according to our data. Variant chr12-14628744-GA-G is described in ClinVar as [Benign]. Clinvar id is 1668452.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-14628744-GA-G is described in Lovd as [Benign].
BS2
?
High Homozygotes in GnomAdExome4 at 4 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GUCY2C | NM_004963.4 | c.2158-8del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000261170.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GUCY2C | ENST00000261170.5 | c.2158-8del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004963.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000803 AC: 121AN: 150766Hom.: 0 Cov.: 0
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GnomAD3 exomes AF: 0.000867 AC: 188AN: 216742Hom.: 1 AF XY: 0.000874 AC XY: 103AN XY: 117828
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GnomAD4 exome AF: 0.000880 AC: 1046AN: 1188842Hom.: 4 Cov.: 20 AF XY: 0.000899 AC XY: 542AN XY: 603030
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GnomAD4 genome ? AF: 0.000802 AC: 121AN: 150880Hom.: 0 Cov.: 0 AF XY: 0.000720 AC XY: 53AN XY: 73614
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 28, 2023 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at