chr1-171334697-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002022.3(FMO4):c.1114G>A(p.Gly372Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00433 in 1,609,836 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002022.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FMO4 | NM_002022.3 | c.1114G>A | p.Gly372Ser | missense_variant | 8/10 | ENST00000367749.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FMO4 | ENST00000367749.4 | c.1114G>A | p.Gly372Ser | missense_variant | 8/10 | 1 | NM_002022.3 | P1 | |
FMO4 | ENST00000480136.1 | n.172G>A | non_coding_transcript_exon_variant | 1/4 | 3 | ||||
FMO4 | ENST00000475780.5 | n.652-2659G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00272 AC: 413AN: 152022Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00245 AC: 599AN: 244656Hom.: 0 AF XY: 0.00244 AC XY: 323AN XY: 132478
GnomAD4 exome AF: 0.00450 AC: 6557AN: 1457696Hom.: 14 Cov.: 31 AF XY: 0.00437 AC XY: 3170AN XY: 725176
GnomAD4 genome ? AF: 0.00271 AC: 413AN: 152140Hom.: 2 Cov.: 32 AF XY: 0.00238 AC XY: 177AN XY: 74374
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 07, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at