chr11-78038743-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001203262.2(NDUFC2-KCTD14):āc.182T>Cā(p.Leu61Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000101 in 1,535,620 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 8/10 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001203262.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDUFC2-KCTD14 | NM_001203262.2 | c.182T>C | p.Leu61Pro | missense_variant | 2/3 | ||
NDUFC2-KCTD14 | NM_001203260.2 | c.326T>C | p.Leu109Pro | missense_variant | 3/4 | ||
KCTD14 | NM_001282406.2 | c.-80T>C | 5_prime_UTR_variant | 2/3 | |||
NDUFC2-KCTD14 | NM_001203261.2 | c.311-21473T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD14 | ENST00000533144.1 | c.-80T>C | 5_prime_UTR_variant | 2/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152236Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000935 AC: 12AN: 128378Hom.: 0 AF XY: 0.0000996 AC XY: 7AN XY: 70296
GnomAD4 exome AF: 0.000109 AC: 151AN: 1383384Hom.: 0 Cov.: 31 AF XY: 0.000123 AC XY: 84AN XY: 682594
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152236Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74392
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2023 | The c.326T>C (p.L109P) alteration is located in exon 3 (coding exon 3) of the NDUFC2-KCTD14 gene. This alteration results from a T to C substitution at nucleotide position 326, causing the leucine (L) at amino acid position 109 to be replaced by a proline (P). 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