20-63244026-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152864.4(NKAIN4):c.530G>A(p.Ser177Asn) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,612,942 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_152864.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NKAIN4 | NM_152864.4 | c.530G>A | p.Ser177Asn | missense_variant, splice_region_variant | 5/7 | ENST00000370316.8 | NP_690603.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NKAIN4 | ENST00000370316.8 | c.530G>A | p.Ser177Asn | missense_variant, splice_region_variant | 5/7 | 1 | NM_152864.4 | ENSP00000359340.3 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152262Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 248334Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134616
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1460562Hom.: 0 Cov.: 30 AF XY: 0.0000220 AC XY: 16AN XY: 726510
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152380Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74518
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 27, 2024 | The c.530G>A (p.S177N) alteration is located in exon 5 (coding exon 5) of the NKAIN4 gene. This alteration results from a G to A substitution at nucleotide position 530, causing the serine (S) at amino acid position 177 to be replaced by an asparagine (N). 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