21-41390601-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_002463.2(MX2):c.769C>A(p.Gln257Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000949 in 1,614,168 control chromosomes in the GnomAD database, including 8 homozygotes. 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 (★).
Frequency
Consequence
NM_002463.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MX2 | NM_002463.2 | c.769C>A | p.Gln257Lys | missense_variant | 6/14 | ENST00000330714.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MX2 | ENST00000330714.8 | c.769C>A | p.Gln257Lys | missense_variant | 6/14 | 1 | NM_002463.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000775 AC: 118AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000879 AC: 221AN: 251482Hom.: 1 AF XY: 0.000898 AC XY: 122AN XY: 135912
GnomAD4 exome AF: 0.000967 AC: 1414AN: 1461866Hom.: 8 Cov.: 30 AF XY: 0.000964 AC XY: 701AN XY: 727232
GnomAD4 genome ? AF: 0.000775 AC: 118AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.000725 AC XY: 54AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.769C>A (p.Q257K) alteration is located in exon 6 (coding exon 5) of the MX2 gene. This alteration results from a C to A substitution at nucleotide position 769, causing the glutamine (Q) at amino acid position 257 to be replaced by a lysine (K). 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