chr6-28260083-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001007531.3(NKAPL):c.712A>G(p.Lys238Glu) variant causes a missense change. The variant allele was found at a frequency of 0.00000253 in 1,579,942 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K238T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001007531.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NKAPL | NM_001007531.3 | c.712A>G | p.Lys238Glu | missense_variant | 1/1 | ENST00000343684.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NKAPL | ENST00000343684.4 | c.712A>G | p.Lys238Glu | missense_variant | 1/1 | NM_001007531.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000140 AC: 2AN: 1427662Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 709362
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 08, 2022 | The c.712A>G (p.K238E) alteration is located in exon 1 (coding exon 1) of the NKAPL gene. This alteration results from a A to G substitution at nucleotide position 712, causing the lysine (K) at amino acid position 238 to be replaced by a glutamic acid (E). 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