chr5-114362977-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_021614.4(KCNN2):c.838G>A(p.Val280Met) variant causes a missense change. The variant allele was found at a frequency of 0.000000695 in 1,438,322 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V280L) has been classified as Uncertain significance.
Frequency
Consequence
NM_021614.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNN2 | NM_021614.4 | c.838G>A | p.Val280Met | missense_variant | 1/8 | ENST00000673685.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNN2 | ENST00000673685.1 | c.838G>A | p.Val280Met | missense_variant | 1/8 | NM_021614.4 | P2 | ||
KCNN2 | ENST00000512097.10 | c.1036G>A | p.Val346Met | missense_variant | 6/13 | 5 | A2 | ||
KCNN2 | ENST00000631899.2 | c.241G>A | p.Val81Met | missense_variant | 1/9 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000469 AC: 1AN: 213422Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 116840
GnomAD4 exome AF: 6.95e-7 AC: 1AN: 1438322Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 715084
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.202G>A (p.V68M) alteration is located in exon 1 (coding exon 1) of the KCNN2 gene. This alteration results from a G to A substitution at nucleotide position 202, causing the valine (V) at amino acid position 68 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at