chr19-51823818-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002030.5(FPR3):c.70G>A(p.Val24Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000471 in 1,613,752 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_002030.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FPR3 | NM_002030.5 | c.70G>A | p.Val24Ile | missense_variant | 2/2 | ENST00000339223.5 | NP_002021.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FPR3 | ENST00000339223.5 | c.70G>A | p.Val24Ile | missense_variant | 2/2 | 1 | NM_002030.5 | ENSP00000341821.3 | ||
FPR3 | ENST00000595991.1 | c.70G>A | p.Val24Ile | missense_variant | 2/2 | 4 | ENSP00000470471.1 | |||
ZNF577 | ENST00000638827.1 | n.*600-12144C>T | intron_variant | 5 | ENSP00000492704.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000120 AC: 30AN: 251032Hom.: 0 AF XY: 0.0000811 AC XY: 11AN XY: 135668
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1461650Hom.: 0 Cov.: 31 AF XY: 0.0000440 AC XY: 32AN XY: 727126
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2022 | The c.70G>A (p.V24I) alteration is located in exon 2 (coding exon 1) of the FPR3 gene. This alteration results from a G to A substitution at nucleotide position 70, causing the valine (V) at amino acid position 24 to be replaced by an isoleucine (I). 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