rs757895735
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_000890.5(KCNJ5):c.795C>T(p.Asp265=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000123 in 1,461,624 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 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
KCNJ5
NM_000890.5 synonymous
NM_000890.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.70
Genes affected
KCNJ5 (HGNC:6266): (potassium inwardly rectifying channel subfamily J member 5) This gene encodes an integral membrane protein which belongs to one of seven subfamilies of inward-rectifier potassium channel proteins called potassium channel subfamily J. The encoded protein is a subunit of the potassium channel which is homotetrameric. It is controlled by G-proteins and has a greater tendency to allow potassium to flow into a cell rather than out of a cell. Naturally occurring mutations in this gene are associated with aldosterone-producing adenomas. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
?
Variant 11-128912068-C-T is Benign according to our data. Variant chr11-128912068-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 514661.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-2.7 with no splicing effect.
BS2
?
High AC in GnomAdExome4 at 18 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNJ5 | NM_000890.5 | c.795C>T | p.Asp265= | synonymous_variant | 2/3 | ENST00000529694.6 | |
KCNJ5 | NM_001354169.2 | c.795C>T | p.Asp265= | synonymous_variant | 3/4 | ||
KCNJ5 | XM_011542810.4 | c.795C>T | p.Asp265= | synonymous_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNJ5 | ENST00000529694.6 | c.795C>T | p.Asp265= | synonymous_variant | 2/3 | 1 | NM_000890.5 | P1 | |
KCNJ5 | ENST00000338350.4 | c.795C>T | p.Asp265= | synonymous_variant | 3/4 | 1 | P1 | ||
KCNJ5 | ENST00000533599.1 | c.795C>T | p.Asp265= | synonymous_variant | 1/2 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 152180Hom.: 0 Cov.: 32 FAILED QC
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GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249620Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135032
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GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461624Hom.: 0 Cov.: 58 AF XY: 0.0000179 AC XY: 13AN XY: 727096
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GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152298Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74474
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 08, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Long QT syndrome 13;C3838758:Familial hyperaldosteronism type III Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 05, 2021 | - - |
Long QT syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 15, 2017 | - - |
Computational scores
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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