16-19714437-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001012991.3(KNOP1):c.599G>A(p.Arg200Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,613,842 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001012991.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KNOP1 | NM_001012991.3 | c.599G>A | p.Arg200Gln | missense_variant | Exon 2 of 5 | ENST00000219837.12 | NP_001013009.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KNOP1 | ENST00000219837.12 | c.599G>A | p.Arg200Gln | missense_variant | Exon 2 of 5 | 1 | NM_001012991.3 | ENSP00000219837.7 | ||
KNOP1 | ENST00000567367.1 | c.140G>A | p.Arg47Gln | missense_variant | Exon 1 of 3 | 3 | ENSP00000455369.1 | |||
KNOP1 | ENST00000565844.1 | n.679G>A | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 | |||||
ENSG00000261312 | ENST00000565916.1 | n.782-349C>T | intron_variant | Intron 1 of 1 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151954Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000360 AC: 9AN: 250304Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135738
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461888Hom.: 0 Cov.: 33 AF XY: 0.0000248 AC XY: 18AN XY: 727242
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151954Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74200
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.599G>A (p.R200Q) alteration is located in exon 2 (coding exon 1) of the KNOP1 gene. This alteration results from a G to A substitution at nucleotide position 599, causing the arginine (R) at amino acid position 200 to be replaced by a glutamine (Q). 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