rs1414209809
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_000486.6(AQP2):c.361-10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,445,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
AQP2
NM_000486.6 intron
NM_000486.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.51
Genes affected
AQP2 (HGNC:634): (aquaporin 2) This gene encodes a water channel protein located in the kidney collecting tubule. It belongs to the MIP/aquaporin family, some members of which are clustered together on chromosome 12q13. Mutations in this gene have been linked to autosomal dominant and recessive forms of nephrogenic diabetes insipidus. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
Variant 12-49954145-C-T is Benign according to our data. Variant chr12-49954145-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1129072.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AQP2 | NM_000486.6 | c.361-10C>T | intron_variant | Intron 1 of 3 | ENST00000199280.4 | NP_000477.1 | ||
AQP5-AS1 | NR_110590.1 | n.460G>A | non_coding_transcript_exon_variant | Exon 2 of 3 | ||||
AQP5-AS1 | NR_110591.1 | n.118-2057G>A | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD3 exomes AF: 0.00000416 AC: 1AN: 240648Hom.: 0 AF XY: 0.00000764 AC XY: 1AN XY: 130900
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GnomAD4 exome AF: 0.0000173 AC: 25AN: 1445802Hom.: 0 Cov.: 30 AF XY: 0.0000153 AC XY: 11AN XY: 719656
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GnomAD4 genome Cov.: 33
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33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Mar 02, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at