chr11-78016633-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_023930.4(KCTD14):c.728T>G(p.Phe243Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,613,992 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.728T>G | p.Phe243Cys | missense_variant | 2/2 | ENST00000353172.6 | |
NDUFC2-KCTD14 | NM_001203262.2 | c.*638T>G | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD14 | ENST00000353172.6 | c.728T>G | p.Phe243Cys | missense_variant | 2/2 | 1 | NM_023930.4 | P1 | |
KCTD14 | ENST00000533144.1 | c.638T>G | p.Phe213Cys | missense_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251334Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135830
GnomAD4 exome AF: 0.000118 AC: 172AN: 1461860Hom.: 0 Cov.: 31 AF XY: 0.0000990 AC XY: 72AN XY: 727228
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | The c.728T>G (p.F243C) alteration is located in exon 2 (coding exon 2) of the KCTD14 gene. This alteration results from a T to G substitution at nucleotide position 728, causing the phenylalanine (F) at amino acid position 243 to be replaced by a cysteine (C). 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