4-158859136-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020840.3(FNIP2):āc.937A>Gā(p.Ile313Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,912 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_020840.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FNIP2 | ENST00000264433.11 | c.937A>G | p.Ile313Val | missense_variant | 9/17 | 1 | NM_020840.3 | ENSP00000264433.6 | ||
FNIP2 | ENST00000512986.5 | c.1006A>G | p.Ile336Val | missense_variant | 9/13 | 1 | ENSP00000421488.1 | |||
FNIP2 | ENST00000504715.1 | c.532A>G | p.Ile178Val | missense_variant | 6/7 | 5 | ENSP00000420841.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152260Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461652Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727096
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74392
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 06, 2024 | The c.937A>G (p.I313V) alteration is located in exon 9 (coding exon 9) of the FNIP2 gene. This alteration results from a A to G substitution at nucleotide position 937, causing the isoleucine (I) at amino acid position 313 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