1-154869723-G-GGCTGCT
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_002249.6(KCNN3):c.236_241dupAGCAGC(p.Gln79_Gln80dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0329 in 1,492,684 control chromosomes in the GnomAD database, including 309 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002249.6 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCNN3 | NM_002249.6 | c.236_241dupAGCAGC | p.Gln79_Gln80dup | conservative_inframe_insertion | Exon 1 of 8 | ENST00000271915.9 | NP_002240.3 | |
KCNN3 | NM_001204087.2 | c.236_241dupAGCAGC | p.Gln79_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.236_241dupAGCAGC | p.Gln79_Gln80dup | conservative_inframe_insertion | Exon 1 of 8 | 1 | NM_002249.6 | ENSP00000271915.3 | ||
KCNN3 | ENST00000618040.4 | c.236_241dupAGCAGC | p.Gln79_Gln80dup | conservative_inframe_insertion | Exon 1 of 9 | 5 | ENSP00000481848.1 |
Frequencies
GnomAD3 genomes AF: 0.0305 AC: 4302AN: 141210Hom.: 88 Cov.: 0
GnomAD4 exome AF: 0.0332 AC: 44866AN: 1351372Hom.: 221 Cov.: 112 AF XY: 0.0328 AC XY: 21927AN XY: 667946
GnomAD4 genome AF: 0.0304 AC: 4302AN: 141312Hom.: 88 Cov.: 0 AF XY: 0.0299 AC XY: 2033AN XY: 67976
ClinVar
Submissions by phenotype
Esophageal atresia;C0034194:Pyloric stenosis Uncertain:1
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not specified Benign:1
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KCNN3-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at