chr11-78016844-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_023930.4(KCTD14):c.517G>C(p.Val173Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000123 in 1,614,084 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_023930.4 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 |
---|---|---|---|---|---|---|---|
KCTD14 | NM_023930.4 | c.517G>C | p.Val173Leu | missense_variant | 2/2 | ENST00000353172.6 | |
NDUFC2-KCTD14 | NM_001203262.2 | c.*427G>C | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD14 | ENST00000353172.6 | c.517G>C | p.Val173Leu | missense_variant | 2/2 | 1 | NM_023930.4 | P1 | |
KCTD14 | ENST00000533144.1 | c.427G>C | p.Val143Leu | missense_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000111 AC: 28AN: 251356Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135854
GnomAD4 exome AF: 0.000120 AC: 176AN: 1461854Hom.: 0 Cov.: 31 AF XY: 0.000111 AC XY: 81AN XY: 727224
GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.517G>C (p.V173L) alteration is located in exon 2 (coding exon 2) of the KCTD14 gene. This alteration results from a G to C substitution at nucleotide position 517, causing the valine (V) at amino acid position 173 to be replaced by a leucine (L). 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