chr2-185739383-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_173651.4(FSIP2):c.137C>T(p.Ala46Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000202 in 1,535,218 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173651.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FSIP2 | ENST00000424728.6 | c.137C>T | p.Ala46Val | missense_variant | Exon 2 of 23 | 5 | NM_173651.4 | ENSP00000401306.1 | ||
FSIP2 | ENST00000465275.1 | n.98C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 | |||||
FSIP2-AS2 | ENST00000427269.2 | n.101+996G>A | intron_variant | Intron 1 of 2 | 5 | |||||
FSIP2-AS1 | ENST00000667756.1 | n.37+49383G>A | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000292 AC: 4AN: 136958Hom.: 0 AF XY: 0.0000404 AC XY: 3AN XY: 74226
GnomAD4 exome AF: 0.0000217 AC: 30AN: 1383062Hom.: 0 Cov.: 31 AF XY: 0.0000249 AC XY: 17AN XY: 682476
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.404C>T (p.A135V) alteration is located in exon 2 (coding exon 2) of the FSIP2 gene. This alteration results from a C to T substitution at nucleotide position 404, causing the alanine (A) at amino acid position 135 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