1-154772331-C-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_002249.6(KCNN3):āc.1092G>Cā(p.Leu364Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 1,613,672 control chromosomes in the GnomAD database, including 282,116 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_002249.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNN3 | ENST00000271915.9 | c.1092G>C | p.Leu364Leu | synonymous_variant | Exon 3 of 8 | 1 | NM_002249.6 | ENSP00000271915.3 | ||
KCNN3 | ENST00000361147.8 | c.177G>C | p.Leu59Leu | synonymous_variant | Exon 3 of 8 | 1 | ENSP00000354764.4 | |||
KCNN3 | ENST00000358505.2 | c.153G>C | p.Leu51Leu | synonymous_variant | Exon 3 of 8 | 1 | ENSP00000351295.2 | |||
KCNN3 | ENST00000618040.4 | c.1092G>C | p.Leu364Leu | synonymous_variant | Exon 3 of 9 | 5 | ENSP00000481848.1 |
Frequencies
GnomAD3 genomes AF: 0.564 AC: 85736AN: 152054Hom.: 24490 Cov.: 34
GnomAD3 exomes AF: 0.581 AC: 145284AN: 250190Hom.: 42601 AF XY: 0.589 AC XY: 79768AN XY: 135318
GnomAD4 exome AF: 0.592 AC: 865456AN: 1461500Hom.: 257612 Cov.: 55 AF XY: 0.595 AC XY: 432451AN XY: 727058
GnomAD4 genome AF: 0.564 AC: 85787AN: 152172Hom.: 24504 Cov.: 34 AF XY: 0.566 AC XY: 42083AN XY: 74400
ClinVar
Submissions by phenotype
not specified Benign:1
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: Frequency -
not provided Benign:1
- -
Zimmermann-laband syndrome 3 Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at