X-119943541-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_024528.4(NKAP):c.65G>C(p.Arg22Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000141 in 1,205,549 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. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024528.4 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 |
---|---|---|---|---|---|---|---|---|---|---|
NKAP | ENST00000371410.5 | c.65G>C | p.Arg22Pro | missense_variant | Exon 1 of 9 | 1 | NM_024528.4 | ENSP00000360464.3 | ||
RHOXF1P3 | ENST00000640298.3 | c.-1236C>G | 5_prime_UTR_variant | Exon 1 of 5 | 5 | ENSP00000515421.1 | ||||
NKAP | ENST00000652253.1 | c.62G>C | p.Arg21Pro | missense_variant | Exon 1 of 9 | ENSP00000498376.1 |
Frequencies
GnomAD3 genomes AF: 0.00000890 AC: 1AN: 112308Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34470
GnomAD3 exomes AF: 0.00000567 AC: 1AN: 176475Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 62747
GnomAD4 exome AF: 0.0000146 AC: 16AN: 1093241Hom.: 0 Cov.: 31 AF XY: 0.0000111 AC XY: 4AN XY: 359323
GnomAD4 genome AF: 0.00000890 AC: 1AN: 112308Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34470
ClinVar
Submissions by phenotype
not provided Uncertain:1
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; Variants in candidate genes are classified as variants of uncertain significance in accordance with ACMG guidelines (Richards et al., 2015) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at