6-39191171-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003740.4(KCNK5):c.1219G>A(p.Ala407Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00335 in 1,614,206 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_003740.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCNK5 | NM_003740.4 | c.1219G>A | p.Ala407Thr | missense_variant | Exon 5 of 5 | ENST00000359534.4 | NP_003731.1 | |
KCNK5 | XM_005249456.2 | c.1210G>A | p.Ala404Thr | missense_variant | Exon 5 of 5 | XP_005249513.1 | ||
KCNK5 | XM_006715235.2 | c.673G>A | p.Ala225Thr | missense_variant | Exon 3 of 3 | XP_006715298.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00328 AC: 500AN: 152212Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.00377 AC: 948AN: 251414Hom.: 6 AF XY: 0.00390 AC XY: 530AN XY: 135900
GnomAD4 exome AF: 0.00336 AC: 4908AN: 1461876Hom.: 15 Cov.: 32 AF XY: 0.00328 AC XY: 2383AN XY: 727242
GnomAD4 genome AF: 0.00328 AC: 500AN: 152330Hom.: 1 Cov.: 31 AF XY: 0.00399 AC XY: 297AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at