chr1-171334658-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002022.3(FMO4):c.1075A>T(p.Asn359Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,613,786 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_002022.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FMO4 | NM_002022.3 | c.1075A>T | p.Asn359Tyr | missense_variant | 8/10 | ENST00000367749.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FMO4 | ENST00000367749.4 | c.1075A>T | p.Asn359Tyr | missense_variant | 8/10 | 1 | NM_002022.3 | P1 | |
FMO4 | ENST00000480136.1 | n.133A>T | non_coding_transcript_exon_variant | 1/4 | 3 | ||||
FMO4 | ENST00000475780.5 | n.652-2698A>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000643 AC: 16AN: 248920Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134746
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461590Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 727118
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 12, 2023 | The c.1075A>T (p.N359Y) alteration is located in exon 8 (coding exon 6) of the FMO4 gene. This alteration results from a A to T substitution at nucleotide position 1075, causing the asparagine (N) at amino acid position 359 to be replaced by a tyrosine (Y). 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