chr9-33294638-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1PM2BP4_Strong
The NM_002504.6(NFX1):āc.244A>Cā(p.Ser82Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000204 in 1,614,096 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 (ā ).
Frequency
Consequence
NM_002504.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFX1 | NM_002504.6 | c.244A>C | p.Ser82Arg | missense_variant | 2/24 | ENST00000379540.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFX1 | ENST00000379540.8 | c.244A>C | p.Ser82Arg | missense_variant | 2/24 | 1 | NM_002504.6 | P1 | |
NFX1 | ENST00000318524.6 | c.244A>C | p.Ser82Arg | missense_variant | 2/16 | 1 | |||
NFX1 | ENST00000379521.8 | n.305A>C | non_coding_transcript_exon_variant | 2/21 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000175 AC: 44AN: 251330Hom.: 0 AF XY: 0.000206 AC XY: 28AN XY: 135812
GnomAD4 exome AF: 0.000219 AC: 320AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.000237 AC XY: 172AN XY: 727244
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 19, 2021 | The c.244A>C (p.S82R) alteration is located in exon 2 (coding exon 2) of the NFX1 gene. This alteration results from a A to C substitution at nucleotide position 244, causing the serine (S) at amino acid position 82 to be replaced by an arginine (R). 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