21-37714359-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_002240.5(KCNJ6):c.798G>A(p.Thr266Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000182 in 1,614,124 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 Benign (★).
Frequency
Genomes: 𝑓 0.00020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00018 ( 0 hom. )
Consequence
KCNJ6
NM_002240.5 synonymous
NM_002240.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.952
Genes affected
KCNJ6 (HGNC:6267): (potassium inwardly rectifying channel subfamily J member 6) This gene encodes a member of the G protein-coupled inwardly-rectifying potassium channel family of inward rectifier potassium channels. This type of potassium channel allows a greater flow of potassium into the cell than out of it. These proteins modulate many physiological processes, including heart rate in cardiac cells and circuit activity in neuronal cells, through G-protein coupled receptor stimulation. Mutations in this gene are associated with Keppen-Lubinsky Syndrome, a rare condition characterized by severe developmental delay, facial dysmorphism, and intellectual disability. [provided by RefSeq, Apr 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 21-37714359-C-T is Benign according to our data. Variant chr21-37714359-C-T is described in ClinVar as [Benign]. Clinvar id is 2155361.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.952 with no splicing effect.
BS2
High AC in GnomAd4 at 30 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152128Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000337 AC: 84AN: 249582Hom.: 0 AF XY: 0.000288 AC XY: 39AN XY: 135404
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GnomAD4 exome AF: 0.000181 AC: 264AN: 1461878Hom.: 0 Cov.: 32 AF XY: 0.000149 AC XY: 108AN XY: 727238
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GnomAD4 genome AF: 0.000197 AC: 30AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74452
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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 | Labcorp Genetics (formerly Invitae), Labcorp | May 11, 2023 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at