rs410837
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000486.6(AQP2):c.607-92A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.977 in 1,233,768 control chromosomes in the GnomAD database, including 593,544 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.89 ( 62498 hom., cov: 33)
Exomes 𝑓: 0.99 ( 531046 hom. )
Consequence
AQP2
NM_000486.6 intron
NM_000486.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.33
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]
AQP5-AS1 (HGNC:55474): (AQP5 and AQP2 antisense RNA 2)
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 12-49955307-A-G is Benign according to our data. Variant chr12-49955307-A-G is described in ClinVar as [Benign]. Clinvar id is 1178280.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AQP2 | NM_000486.6 | c.607-92A>G | intron_variant | ENST00000199280.4 | |||
AQP5-AS1 | NR_110591.1 | n.118-3219T>C | intron_variant, non_coding_transcript_variant | ||||
AQP5-AS1 | NR_110590.1 | n.257-959T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AQP2 | ENST00000199280.4 | c.607-92A>G | intron_variant | 1 | NM_000486.6 | P1 | |||
AQP5-AS1 | ENST00000550530.1 | n.118-3219T>C | intron_variant, non_coding_transcript_variant | 3 | |||||
ENST00000552806.1 | n.541+278T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.890 AC: 135419AN: 152146Hom.: 62465 Cov.: 33
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GnomAD4 exome AF: 0.989 AC: 1069817AN: 1081504Hom.: 531046 AF XY: 0.991 AC XY: 534533AN XY: 539634
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GnomAD4 genome ? AF: 0.890 AC: 135502AN: 152264Hom.: 62498 Cov.: 33 AF XY: 0.894 AC XY: 66525AN XY: 74454
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 10, 2021 | - - |
Diabetes insipidus, nephrogenic, autosomal Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 10, 2021 | - - |
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