X-102360627-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001099686.3(NXF2B):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. 10/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001099686.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NXF2B | ENST00000602195.6 | c.1855G>A | p.Ala619Thr | missense_variant | Exon 23 of 23 | 1 | NM_001099686.3 | ENSP00000472530.1 | ||
ENSG00000284800 | ENST00000618302.2 | n.*2228G>A | non_coding_transcript_exon_variant | Exon 27 of 27 | 2 | ENSP00000484645.2 | ||||
ENSG00000284800 | ENST00000618302.2 | n.*2228G>A | 3_prime_UTR_variant | Exon 27 of 27 | 2 | ENSP00000484645.2 |
Frequencies
GnomAD3 genomes Cov.: 0
GnomAD3 exomes AF: 0.0000973 AC: 14AN: 143934Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 44440
GnomAD4 exome Cov.: 0
GnomAD4 genome Cov.: 0
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1855G>A (p.A619T) alteration is located in exon 23 (coding exon 21) of the NXF2B 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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at