14-24431661-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015299.3(KHNYN):c.400C>T(p.Arg134Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000564 in 1,613,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015299.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KHNYN | ENST00000553935.6 | c.400C>T | p.Arg134Trp | missense_variant | Exon 3 of 8 | 1 | NM_015299.3 | ENSP00000450799.1 | ||
KHNYN | ENST00000251343.9 | c.400C>T | p.Arg134Trp | missense_variant | Exon 3 of 8 | 1 | ENSP00000251343.5 | |||
KHNYN | ENST00000556842.5 | c.400C>T | p.Arg134Trp | missense_variant | Exon 3 of 8 | 2 | ENSP00000451106.1 | |||
KHNYN | ENST00000556510.1 | c.400C>T | p.Arg134Trp | missense_variant | Exon 2 of 2 | 2 | ENSP00000451004.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251164Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135812
GnomAD4 exome AF: 0.0000568 AC: 83AN: 1461766Hom.: 0 Cov.: 30 AF XY: 0.0000536 AC XY: 39AN XY: 727186
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.400C>T (p.R134W) alteration is located in exon 3 (coding exon 2) of the KHNYN gene. This alteration results from a C to T substitution at nucleotide position 400, causing the arginine (R) at amino acid position 134 to be replaced by a tryptophan (W). 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