Variant 1-171283148-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001282693.2(FMO1):c.1188A>G(p.Val396Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,538,742 control chromosomes in the GnomAD database, including 23,758 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.24 ( 6923 hom., cov: 30)

Exomes 𝑓: 0.14 ( 16835 hom. )

Consequence

FMO1
NM_001282693.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.87

Variant links:

Genes affected

FMO1 (HGNC:3769): (flavin containing dimethylaniline monoxygenase 1) Metabolic N-oxidation of the diet-derived amino-trimethylamine (TMA) is mediated by flavin-containing monooxygenase and is subject to an inherited FMO3 polymorphism in man resulting in a small subpopulation with reduced TMA N-oxidation capacity resulting in fish odor syndrome Trimethylaminuria. Three forms of the enzyme, FMO1 found in fetal liver, FMO2 found in adult liver, and FMO3 are encoded by genes clustered in the 1q23-q25 region. Flavin-containing monooxygenases are NADPH-dependent flavoenzymes that catalyzes the oxidation of soft nucleophilic heteroatom centers in drugs, pesticides, and xenobiotics. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]

FMO1 links:

FMO1 (HGNC:):

FMO1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 1-171283148-A-G is Benign according to our data. Variant chr1-171283148-A-G is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-2.87 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FMO1	NM_001282693.2 linkuse as main transcript	c.1188A>G	p.Val396Val	synonymous_variant	8/9	ENST00000617670.6	NP_001269622.1	Q01740-1A0A024R934B2RCG5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FMO1	ENST00000617670.6 linkuse as main transcript	c.1188A>G	p.Val396Val	synonymous_variant	8/9	1	NM_001282693.2	ENSP00000481732.1		Q01740-1

Frequencies

GnomAD3 genomes

AF:

0.241

AC:

36542

AN:

151566

Hom.:

6917

Cov.:

show subpopulations

Gnomad AFR

AF:

0.532

Gnomad AMI

AF:

0.0800

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.140

Gnomad EAS

AF:

0.0324

Gnomad SAS

AF:

0.188

Gnomad FIN

AF:

0.124

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.138

Gnomad OTH

AF:

0.207

GnomAD3 exomes

AF:

0.152

AC:

35794

AN:

235056

Hom.:

4280

AF XY:

0.150

AC XY:

19119

AN XY:

127464

show subpopulations

Gnomad AFR exome

AF:

0.541

Gnomad AMR exome

AF:

0.0792

Gnomad ASJ exome

AF:

0.128

Gnomad EAS exome

AF:

0.0294

Gnomad SAS exome

AF:

0.179

Gnomad FIN exome

AF:

0.127

Gnomad NFE exome

AF:

0.139

Gnomad OTH exome

AF:

0.137

GnomAD4 exome

AF:

0.139

AC:

192484

AN:

1387060

Hom.:

16835

Cov.:

AF XY:

0.140

AC XY:

96881

AN XY:

693472

show subpopulations

Gnomad4 AFR exome

AF:

0.536

Gnomad4 AMR exome

AF:

0.0865

Gnomad4 ASJ exome

AF:

0.127

Gnomad4 EAS exome

AF:

0.0224

Gnomad4 SAS exome

AF:

0.173

Gnomad4 FIN exome

AF:

0.124

Gnomad4 NFE exome

AF:

0.131

Gnomad4 OTH exome

AF:

0.152

GnomAD4 genome

AF:

0.241

AC:

36568

AN:

151682

Hom.:

6923

Cov.:

AF XY:

0.237

AC XY:

17548

AN XY:

74138

show subpopulations

Gnomad4 AFR

AF:

0.531

Gnomad4 AMR

AF:

0.124

Gnomad4 ASJ

AF:

0.140

Gnomad4 EAS

AF:

0.0327

Gnomad4 SAS

AF:

0.187

Gnomad4 FIN

AF:

0.124

Gnomad4 NFE

AF:

0.138

Gnomad4 OTH

AF:

0.204

Alfa

AF:

0.157

Hom.:

3009

Bravo

AF:

0.251

Asia WGS

AF:

0.130

AC:

454

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.17

DANN

Benign

0.59

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over