chr6-116689357-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001366306.2(KPNA5):c.42G>A(p.Met14Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000104 in 1,608,288 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 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. M14L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001366306.2 missense
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 | UniProt |
---|---|---|---|---|---|---|---|
KPNA5 | NM_001366306.2 | c.42G>A | p.Met14Ile | missense_variant | 2/14 | ENST00000368564.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KPNA5 | ENST00000368564.7 | c.42G>A | p.Met14Ile | missense_variant | 2/14 | 1 | NM_001366306.2 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000488 AC: 12AN: 245900Hom.: 0 AF XY: 0.0000526 AC XY: 7AN XY: 133080
GnomAD4 exome AF: 0.000110 AC: 160AN: 1456214Hom.: 0 Cov.: 30 AF XY: 0.0000994 AC XY: 72AN XY: 724448
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74288
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2021 | The c.42G>A (p.M14I) alteration is located in exon 2 (coding exon 2) of the KPNA5 gene. This alteration results from a G to A substitution at nucleotide position 42, causing the methionine (M) at amino acid position 14 to be replaced by an isoleucine (I). 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