chr15-32798936-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001277313.2(FMN1):c.3998G>A(p.Arg1333Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,613,014 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001277313.2 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 |
---|---|---|---|---|---|---|---|
FMN1 | NM_001277313.2 | c.3998G>A | p.Arg1333Gln | missense_variant | 19/21 | ENST00000616417.5 | |
LOC107984089 | XR_002957769.2 | n.198-11982C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FMN1 | ENST00000616417.5 | c.3998G>A | p.Arg1333Gln | missense_variant | 19/21 | 5 | NM_001277313.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 151988Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000133 AC: 33AN: 247942Hom.: 0 AF XY: 0.000179 AC XY: 24AN XY: 134454
GnomAD4 exome AF: 0.000112 AC: 163AN: 1461026Hom.: 0 Cov.: 32 AF XY: 0.000127 AC XY: 92AN XY: 726718
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 151988Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 5AN XY: 74220
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 04, 2024 | The c.3329G>A (p.R1110Q) alteration is located in exon 15 (coding exon 15) of the FMN1 gene. This alteration results from a G to A substitution at nucleotide position 3329, causing the arginine (R) at amino acid position 1110 to be replaced by a glutamine (Q). 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