9-33294618-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002504.6(NFX1):c.224C>T(p.Pro75Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,614,038 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_002504.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NFX1 | ENST00000379540.8 | c.224C>T | p.Pro75Leu | missense_variant | Exon 2 of 24 | 1 | NM_002504.6 | ENSP00000368856.3 | ||
NFX1 | ENST00000318524.6 | c.224C>T | p.Pro75Leu | missense_variant | Exon 2 of 16 | 1 | ENSP00000317695.6 | |||
NFX1 | ENST00000379521.8 | n.285C>T | non_coding_transcript_exon_variant | Exon 2 of 21 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251358Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135830
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 727238
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.224C>T (p.P75L) alteration is located in exon 2 (coding exon 2) of the NFX1 gene. This alteration results from a C to T substitution at nucleotide position 224, causing the proline (P) at amino acid position 75 to be replaced by a leucine (L). 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