chr1-171334538-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002022.3(FMO4):c.955G>A(p.Glu319Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,613,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002022.3 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 | UniProt |
---|---|---|---|---|---|---|---|
FMO4 | NM_002022.3 | c.955G>A | p.Glu319Lys | missense_variant | 8/10 | ENST00000367749.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FMO4 | ENST00000367749.4 | c.955G>A | p.Glu319Lys | missense_variant | 8/10 | 1 | NM_002022.3 | P1 | |
FMO4 | ENST00000480136.1 | n.13G>A | non_coding_transcript_exon_variant | 1/4 | 3 | ||||
FMO4 | ENST00000475780.5 | n.652-2818G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000171 AC: 43AN: 250982Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135644
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461492Hom.: 0 Cov.: 31 AF XY: 0.0000468 AC XY: 34AN XY: 727058
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 02, 2023 | The c.955G>A (p.E319K) alteration is located in exon 8 (coding exon 6) of the FMO4 gene. This alteration results from a G to A substitution at nucleotide position 955, causing the glutamic acid (E) at amino acid position 319 to be replaced by a lysine (K). 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