rs1839318
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_001650.7(AQP4):c.492G>A(p.Leu164=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0233 in 1,614,006 control chromosomes in the GnomAD database, including 799 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 0.025 ( 69 hom., cov: 33)
Exomes 𝑓: 0.023 ( 730 hom. )
Consequence
AQP4
NM_001650.7 synonymous
NM_001650.7 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.02
Genes affected
AQP4 (HGNC:637): (aquaporin 4) This gene encodes a member of the aquaporin family of intrinsic membrane proteins that function as water-selective channels in the plasma membranes of many cells. This protein is the predominant aquaporin found in brain and has an important role in brain water homeostasis. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. Additional isoforms, resulting from the use of alternative in-frame translation initiation codons, have also been described. Recent studies provided evidence for translational readthrough in this gene, and expression of C-terminally extended isoforms via the use of an alternative in-frame translation termination codon. [provided by RefSeq, Jun 2018]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP7
?
Synonymous conserved (PhyloP=2.02 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.091 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AQP4 | NM_001650.7 | c.492G>A | p.Leu164= | synonymous_variant | 3/5 | ENST00000383168.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AQP4 | ENST00000383168.9 | c.492G>A | p.Leu164= | synonymous_variant | 3/5 | 1 | NM_001650.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0247 AC: 3753AN: 152182Hom.: 70 Cov.: 33
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GnomAD3 exomes AF: 0.0286 AC: 7180AN: 251384Hom.: 215 AF XY: 0.0329 AC XY: 4468AN XY: 135868
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GnomAD4 exome AF: 0.0232 AC: 33931AN: 1461706Hom.: 730 Cov.: 31 AF XY: 0.0255 AC XY: 18517AN XY: 727160
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GnomAD4 genome ? AF: 0.0246 AC: 3753AN: 152300Hom.: 69 Cov.: 33 AF XY: 0.0268 AC XY: 1993AN XY: 74468
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at