chrX-102321860-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_022053.4(NXF2):c.1270G>A(p.Ala424Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A424V) has been classified as Uncertain significance.
Frequency
Consequence
NM_022053.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NXF2 | NM_022053.4 | c.1270G>A | p.Ala424Thr | missense_variant | 16/23 | ENST00000625106.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NXF2 | ENST00000625106.4 | c.1270G>A | p.Ala424Thr | missense_variant | 16/23 | 1 | NM_022053.4 | P1 | |
NXF2 | ENST00000604790.2 | c.1270G>A | p.Ala424Thr | missense_variant | 14/21 | 1 | P1 |
Frequencies
GnomAD3 genomes Cov.: 0
GnomAD3 exomes AF: 0.0000489 AC: 7AN: 143179Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 45405
GnomAD4 exome Cov.: 0
GnomAD4 genome Cov.: 0
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at