rs3741559
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_000486.6(AQP2):c.360+3G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 1,600,584 control chromosomes in the GnomAD database, including 30,538 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000486.6 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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AQP2 | ENST00000199280.4 | c.360+3G>A | splice_region_variant, intron_variant | Intron 1 of 3 | 1 | NM_000486.6 | ENSP00000199280.3 | |||
AQP2 | ENST00000550862.1 | c.360+3G>A | splice_region_variant, intron_variant | Intron 1 of 2 | 5 | ENSP00000450022.1 | ||||
AQP2 | ENST00000551526.5 | n.360+3G>A | splice_region_variant, intron_variant | Intron 1 of 5 | 5 | ENSP00000447148.1 |
Frequencies
GnomAD3 genomes AF: 0.170 AC: 25929AN: 152132Hom.: 2539 Cov.: 33
GnomAD3 exomes AF: 0.197 AC: 45710AN: 232494Hom.: 5294 AF XY: 0.206 AC XY: 26032AN XY: 126564
GnomAD4 exome AF: 0.188 AC: 272814AN: 1448332Hom.: 28003 Cov.: 33 AF XY: 0.193 AC XY: 138660AN XY: 719146
GnomAD4 genome AF: 0.170 AC: 25920AN: 152252Hom.: 2535 Cov.: 33 AF XY: 0.173 AC XY: 12841AN XY: 74412
ClinVar
Submissions by phenotype
Diabetes insipidus, nephrogenic, autosomal Benign:4
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
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not provided Benign:3
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This variant is associated with the following publications: (PMID: 27884173, 20814834) -
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not specified Benign:2
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Nephrogenic diabetes insipidus Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at