ENST00000688521.1:c.2123G>A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000688521.1(NKRF):c.2123G>A(p.Arg708His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000133 in 1,203,288 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes 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
ENST00000688521.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NKRF | ENST00000688521.1 | c.2123G>A | p.Arg708His | missense_variant | Exon 4 of 4 | ENSP00000508667.1 |
Frequencies
GnomAD3 genomes AF: 0.0000190 AC: 2AN: 105418Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 29026
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183437Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67881
GnomAD4 exome AF: 0.0000128 AC: 14AN: 1097870Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 4AN XY: 363252
GnomAD4 genome AF: 0.0000190 AC: 2AN: 105418Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 29026
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1889G>A (p.R630H) alteration is located in exon 4 (coding exon 3) of the NKRF gene. This alteration results from a G to A substitution at nucleotide position 1889, causing the arginine (R) at amino acid position 630 to be replaced by a histidine (H). 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