chrX-102326488-G-A
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_022053.4(NXF2):c.1855G>A(p.Ala619Thr) 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 (★). Synonymous variant affecting the same amino acid position (i.e. A619A) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 0)
Consequence
NXF2
NM_022053.4 missense
NM_022053.4 missense
Scores
2
9
Clinical Significance
Conservation
PhyloP100: 1.39
Genes affected
NXF2 (HGNC:8072): (nuclear RNA export factor 2) This gene encodes a member of a family of nuclear RNA export proteins. The encoded protein is associated with the nuclear envelope and aids in the export of mRNAs. There is a closely related paralog of this gene located adjacent on chromosome X and on the opposite strand. [provided by RefSeq, Aug 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.09921217).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NXF2 | NM_022053.4 | c.1855G>A | p.Ala619Thr | missense_variant | 23/23 | ENST00000625106.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NXF2 | ENST00000625106.4 | c.1855G>A | p.Ala619Thr | missense_variant | 23/23 | 1 | NM_022053.4 | P1 | |
NXF2 | ENST00000604790.2 | c.1855G>A | p.Ala619Thr | missense_variant | 21/21 | 1 | P1 |
Frequencies
GnomAD3 genomes Cov.: 0
GnomAD3 genomes
Cov.:
0
GnomAD3 exomes AF: 0.0000564 AC: 5AN: 88704Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 24096
GnomAD3 exomes
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5
AN:
88704
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0
AN XY:
24096
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GnomAD4 exome Cov.: 0
GnomAD4 exome
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0
GnomAD4 genome Cov.: 0
GnomAD4 genome
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0
ESP6500AA
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1
ESP6500EA
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1
ExAC
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3
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2022 | The c.1855G>A (p.A619T) alteration is located in exon 23 (coding exon 21) of the NXF2 gene. This alteration results from a G to A substitution at nucleotide position 1855, causing the alanine (A) at amino acid position 619 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T
FATHMM_MKL
Benign
N
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N
PrimateAI
Benign
T
Sift4G
Uncertain
D;D
Polyphen
P;P
Vest4
MVP
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at