rs1049305
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198098.4(AQP1):c.*578G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
AQP1
NM_198098.4 3_prime_UTR
NM_198098.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.337
Genes affected
AQP1 (HGNC:633): (aquaporin 1 (Colton blood group)) This gene encodes a small integral membrane protein with six bilayer spanning domains that functions as a water channel protein. This protein permits passive transport of water along an osmotic gradient. This gene is a possible candidate for disorders involving imbalance in ocular fluid movement. [provided by RefSeq, Aug 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AQP1 | NM_198098.4 | c.*578G>A | 3_prime_UTR_variant | 4/4 | ENST00000311813.11 | ||
AQP1 | NM_001329872.2 | c.*198G>A | 3_prime_UTR_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AQP1 | ENST00000311813.11 | c.*578G>A | 3_prime_UTR_variant | 4/4 | 1 | NM_198098.4 | P1 | ||
AQP1 | ENST00000441328.7 | n.522G>A | non_coding_transcript_exon_variant | 2/2 | 1 | ||||
AQP1 | ENST00000652696.1 | c.*405G>A | 3_prime_UTR_variant | 5/5 | P1 | ||||
AQP1 | ENST00000652692.1 | c.*24+554G>A | intron_variant |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 790104Hom.: 0 Cov.: 10 AF XY: 0.00 AC XY: 0AN XY: 377662
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
790104
Hom.:
Cov.:
10
AF XY:
AC XY:
0
AN XY:
377662
Gnomad4 AFR exome
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Gnomad4 OTH exome
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GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Calibrated prediction
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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