7-30912239-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_198098.4(AQP1):c.330C>T(p.Ala110Ala) variant causes a synonymous 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. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
AQP1
NM_198098.4 synonymous
NM_198098.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.272
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 -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 7-30912239-C-T is Benign according to our data. Variant chr7-30912239-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3618873.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.272 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AQP1 | NM_198098.4 | c.330C>T | p.Ala110Ala | synonymous_variant | Exon 1 of 4 | ENST00000311813.11 | NP_932766.1 | |
AQP1 | NM_001329872.2 | c.330C>T | p.Ala110Ala | synonymous_variant | Exon 1 of 5 | NP_001316801.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AQP1 | ENST00000311813.11 | c.330C>T | p.Ala110Ala | synonymous_variant | Exon 1 of 4 | 1 | NM_198098.4 | ENSP00000311165.4 | ||
ENSG00000250424 | ENST00000509504.2 | c.867C>T | p.Ala289Ala | synonymous_variant | Exon 8 of 11 | 5 | ENSP00000421315.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1456154Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 724724
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
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0
AN:
1456154
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Cov.:
32
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AC XY:
0
AN XY:
724724
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Feb 02, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational 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