6-39191441-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003740.4(KCNK5):āc.949G>Cā(p.Gly317Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,406 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_003740.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNK5 | NM_003740.4 | c.949G>C | p.Gly317Arg | missense_variant | 5/5 | ENST00000359534.4 | |
KCNK5 | XM_005249456.2 | c.940G>C | p.Gly314Arg | missense_variant | 5/5 | ||
KCNK5 | XM_006715235.2 | c.403G>C | p.Gly135Arg | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNK5 | ENST00000359534.4 | c.949G>C | p.Gly317Arg | missense_variant | 5/5 | 1 | NM_003740.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151990Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250832Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135672
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461298Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727000
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152108Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2023 | The c.949G>C (p.G317R) alteration is located in exon 5 (coding exon 5) of the KCNK5 gene. This alteration results from a G to C substitution at nucleotide position 949, causing the glycine (G) at amino acid position 317 to be replaced by an arginine (R). 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