chr16-25217245-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001169.3(AQP8):c.60G>A(p.Pro20=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00227 in 1,614,206 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0088 ( 20 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 17 hom. )
Consequence
AQP8
NM_001169.3 synonymous
NM_001169.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.336
Genes affected
AQP8 (HGNC:642): (aquaporin 8) Aquaporin 8 (AQP8) is a water channel protein. Aquaporins are a family of small integral membrane proteins related to the major intrinsic protein (MIP or AQP0). Aquaporin 8 mRNA is found in pancreas and colon but not other tissues. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 16-25217245-G-A is Benign according to our data. Variant chr16-25217245-G-A is described in ClinVar as [Benign]. Clinvar id is 778581.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.336 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00879 (1339/152324) while in subpopulation AFR AF= 0.0271 (1125/41564). AF 95% confidence interval is 0.0258. There are 20 homozygotes in gnomad4. There are 641 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 20 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AQP8 | NM_001169.3 | c.60G>A | p.Pro20= | synonymous_variant | 2/6 | ENST00000219660.6 | |
AQP8 | XM_011545822.3 | c.63G>A | p.Pro21= | synonymous_variant | 2/6 | ||
AQP8 | XM_011545823.3 | c.63G>A | p.Pro21= | synonymous_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AQP8 | ENST00000219660.6 | c.60G>A | p.Pro20= | synonymous_variant | 2/6 | 1 | NM_001169.3 | P4 | |
AQP8 | ENST00000566125.5 | c.42G>A | p.Pro14= | synonymous_variant | 2/6 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00876 AC: 1334AN: 152206Hom.: 20 Cov.: 32
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GnomAD3 exomes AF: 0.00309 AC: 777AN: 251388Hom.: 5 AF XY: 0.00265 AC XY: 360AN XY: 135852
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GnomAD4 exome AF: 0.00159 AC: 2331AN: 1461882Hom.: 17 Cov.: 31 AF XY: 0.00152 AC XY: 1107AN XY: 727242
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GnomAD4 genome ? AF: 0.00879 AC: 1339AN: 152324Hom.: 20 Cov.: 32 AF XY: 0.00860 AC XY: 641AN XY: 74496
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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 | Invitae | Jun 08, 2018 | - - |
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