chr1-154869723-G-GGCTGCTGCT
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
The NM_002249.6(KCNN3):c.233_241dupAGCAGCAGC(p.Gln78_Gln80dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002249.6 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCNN3 | NM_002249.6 | c.233_241dupAGCAGCAGC | p.Gln78_Gln80dup | conservative_inframe_insertion | Exon 1 of 8 | ENST00000271915.9 | NP_002240.3 | |
KCNN3 | NM_001204087.2 | c.233_241dupAGCAGCAGC | p.Gln78_Gln80dup | conservative_inframe_insertion | Exon 1 of 9 | NP_001191016.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNN3 | ENST00000271915.9 | c.233_241dupAGCAGCAGC | p.Gln78_Gln80dup | conservative_inframe_insertion | Exon 1 of 8 | 1 | NM_002249.6 | ENSP00000271915.3 | ||
KCNN3 | ENST00000618040.4 | c.233_241dupAGCAGCAGC | p.Gln78_Gln80dup | conservative_inframe_insertion | Exon 1 of 9 | 5 | ENSP00000481848.1 |
Frequencies
GnomAD3 genomes AF: 0.134 AC: 18884AN: 140982Hom.: 1518 Cov.: 0
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.119 AC: 156714AN: 1321026Hom.: 2021 Cov.: 112 AF XY: 0.119 AC XY: 77685AN XY: 653388
GnomAD4 genome AF: 0.134 AC: 18902AN: 141082Hom.: 1519 Cov.: 0 AF XY: 0.135 AC XY: 9167AN XY: 67870
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:1
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Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Not present in ESP. LOF is NOT an established disease mechanism. Not enough evidence that the gene is associated with cardiomyopathy. Mice homozygous for a conditional gene switch displayed no overt phenotype. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at