chrX-102321861-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_022053.4(NXF2):c.1271C>T(p.Ala424Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 9/14 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. A424T) has been classified as Likely benign.
Frequency
Consequence
NM_022053.4 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 |
---|---|---|---|---|---|---|---|
NXF2 | NM_022053.4 | c.1271C>T | p.Ala424Val | missense_variant | 16/23 | ENST00000625106.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NXF2 | ENST00000625106.4 | c.1271C>T | p.Ala424Val | missense_variant | 16/23 | 1 | NM_022053.4 | P1 | |
NXF2 | ENST00000604790.2 | c.1271C>T | p.Ala424Val | missense_variant | 14/21 | 1 | P1 |
Frequencies
GnomAD3 genomes Cov.: 0
GnomAD4 exome Cov.: 0
GnomAD4 genome Cov.: 0
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.1271C>T (p.A424V) alteration is located in exon 16 (coding exon 14) of the NXF2 gene. This alteration results from a C to T substitution at nucleotide position 1271, causing the alanine (A) at amino acid position 424 to be replaced by a valine (V). 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