chr18-26856289-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001650.7(AQP4):c.894G>A(p.Val298=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00027 in 1,614,212 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0015 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00015 ( 0 hom. )
Consequence
AQP4
NM_001650.7 synonymous
NM_001650.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.441
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 Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
Variant 18-26856289-C-T is Benign according to our data. Variant chr18-26856289-C-T is described in ClinVar as [Benign]. Clinvar id is 715091.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.441 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AQP4 | NM_001650.7 | c.894G>A | p.Val298= | synonymous_variant | 5/5 | ENST00000383168.9 | NP_001641.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AQP4 | ENST00000383168.9 | c.894G>A | p.Val298= | synonymous_variant | 5/5 | 1 | NM_001650.7 | ENSP00000372654 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00145 AC: 220AN: 152208Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000449 AC: 113AN: 251488Hom.: 1 AF XY: 0.000361 AC XY: 49AN XY: 135916
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GnomAD4 exome AF: 0.000147 AC: 215AN: 1461886Hom.: 0 Cov.: 31 AF XY: 0.000138 AC XY: 100AN XY: 727246
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GnomAD4 genome AF: 0.00145 AC: 221AN: 152326Hom.: 1 Cov.: 33 AF XY: 0.00144 AC XY: 107AN XY: 74492
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
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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