X-119590463-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001417890.1(NKRF):c.1241G>T(p.Gly414Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000165 in 1,209,701 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001417890.1 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 |
---|---|---|---|---|---|---|---|---|---|---|
NKRF | ENST00000688521.1 | c.1241G>T | p.Gly414Val | missense_variant | Exon 4 of 4 | ENSP00000508667.1 |
Frequencies
GnomAD3 genomes AF: 0.00000896 AC: 1AN: 111617Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33807
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1098084Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 363444
GnomAD4 genome AF: 0.00000896 AC: 1AN: 111617Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33807
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1007G>T (p.G336V) alteration is located in exon 4 (coding exon 3) of the NKRF gene. This alteration results from a G to T substitution at nucleotide position 1007, causing the glycine (G) at amino acid position 336 to be replaced by a valine (V). 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