5-144474024-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020768.4(KCTD16):c.1197C>G(p.Ile399Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 151,994 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020768.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCTD16 | NM_020768.4 | c.1197C>G | p.Ile399Met | missense_variant | Exon 4 of 4 | ENST00000512467.6 | NP_065819.1 | |
KCTD16 | NM_001370486.1 | c.1197C>G | p.Ile399Met | missense_variant | Exon 3 of 3 | NP_001357415.1 | ||
KCTD16 | NM_001370487.1 | c.1197C>G | p.Ile399Met | missense_variant | Exon 3 of 3 | NP_001357416.1 | ||
KCTD16 | XM_005268493.3 | c.1197C>G | p.Ile399Met | missense_variant | Exon 3 of 3 | XP_005268550.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151994Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151994Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74208
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1197C>G (p.I399M) alteration is located in exon 4 (coding exon 2) of the KCTD16 gene. This alteration results from a C to G substitution at nucleotide position 1197, causing the isoleucine (I) at amino acid position 399 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