7-30912215-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_198098.4(AQP1):c.306C>T(p.Cys102Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000621 in 1,610,850 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000064 ( 0 hom. )
Consequence
AQP1
NM_198098.4 synonymous
NM_198098.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.278
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 -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
Variant 7-30912215-C-T is Benign according to our data. Variant chr7-30912215-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3662498.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.278 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AQP1 | NM_198098.4 | c.306C>T | p.Cys102Cys | synonymous_variant | Exon 1 of 4 | ENST00000311813.11 | NP_932766.1 | |
AQP1 | NM_001329872.2 | c.306C>T | p.Cys102Cys | 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.306C>T | p.Cys102Cys | synonymous_variant | Exon 1 of 4 | 1 | NM_198098.4 | ENSP00000311165.4 | ||
ENSG00000250424 | ENST00000509504.2 | c.843C>T | p.Cys281Cys | synonymous_variant | Exon 8 of 11 | 5 | ENSP00000421315.2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152110Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000563 AC: 14AN: 248618Hom.: 0 AF XY: 0.0000520 AC XY: 7AN XY: 134670
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GnomAD4 exome AF: 0.0000644 AC: 94AN: 1458740Hom.: 0 Cov.: 32 AF XY: 0.0000592 AC XY: 43AN XY: 725870
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GnomAD4 genome AF: 0.0000394 AC: 6AN: 152110Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74302
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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
May 16, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at