chr1-171332743-T-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002022.3(FMO4):c.662T>A(p.Leu221His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00449 in 1,611,478 control chromosomes in the GnomAD database, including 25 homozygotes. 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 Likely benign (★).
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.662T>A | p.Leu221His | missense_variant | 7/10 | ENST00000367749.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FMO4 | ENST00000367749.4 | c.662T>A | p.Leu221His | missense_variant | 7/10 | 1 | NM_002022.3 | P1 | |
FMO4 | ENST00000462992.1 | n.428T>A | non_coding_transcript_exon_variant | 4/4 | 3 | ||||
FMO4 | ENST00000475780.5 | n.652-4613T>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00331 AC: 504AN: 152202Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00307 AC: 771AN: 251114Hom.: 3 AF XY: 0.00298 AC XY: 404AN XY: 135700
GnomAD4 exome AF: 0.00461 AC: 6725AN: 1459158Hom.: 22 Cov.: 29 AF XY: 0.00432 AC XY: 3136AN XY: 726118
GnomAD4 genome ? AF: 0.00331 AC: 504AN: 152320Hom.: 3 Cov.: 32 AF XY: 0.00320 AC XY: 238AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at