Variant chr1-171209118-C-CT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001460.5(FMO2):c.1588dup(p.Cys530LeufsTer30) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 678,584 control chromosomes in the GnomAD database, including 4,860 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.11 ( 1033 hom., cov: 30)

Exomes 𝑓: 0.10 ( 3827 hom. )

Consequence

FMO2
NM_001460.5 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.47

Variant links:

Genes affected

FMO2 (HGNC:3770): (flavin containing dimethylaniline monoxygenase 2) This gene encodes a flavin-containing monooxygenase family member. It is an NADPH-dependent enzyme that catalyzes the N-oxidation of some primary alkylamines through an N-hydroxylamine intermediate. However, some human populations contain an allele (FMO2*2A) with a premature stop codon, resulting in a protein that is C-terminally-truncated, has no catalytic activity, and is likely degraded rapidly. This gene is found in a cluster with other related family members on chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2014]

FMO2 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 1-171209118-C-CT is Benign according to our data. Variant chr1-171209118-C-CT is described in ClinVar as [Benign]. Clinvar id is 767726.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
FMO2	NM_001460.5 linkuse as main transcript	c.1588dup	p.Cys530LeufsTer30	frameshift_variant	9/9	ENST00000209929.10
LOC124900413	XR_007066731.1 linkuse as main transcript	n.366-12181_366-12180insA		intron_variant, non_coding_transcript_variant
LOC105371611	XR_922278.4 linkuse as main transcript	n.514+38462_514+38463insA		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
FMO2	ENST00000209929.10 linkuse as main transcript	c.1588dup	p.Cys530LeufsTer30	frameshift_variant	9/9	1	NM_001460.5	P1
	ENST00000445290.1 linkuse as main transcript	n.139-9604_139-9603insA		intron_variant, non_coding_transcript_variant		2
	ENST00000669750.1 linkuse as main transcript	n.448+38447_448+38448insA		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.108

AC:

16345

AN:

151154

Hom.:

1030

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0956

Gnomad AMI

AF:

0.0473

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.141

Gnomad EAS

AF:

0.244

Gnomad SAS

AF:

0.236

Gnomad FIN

AF:

0.0699

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.0881

Gnomad OTH

AF:

0.106

GnomAD4 exome

AF:

0.104

AC:

54593

AN:

527316

Hom.:

3827

Cov.:

AF XY:

0.107

AC XY:

29563

AN XY:

275144

show subpopulations

Gnomad4 AFR exome

AF:

0.0866

Gnomad4 AMR exome

AF:

0.186

Gnomad4 ASJ exome

AF:

0.139

Gnomad4 EAS exome

AF:

0.243

Gnomad4 SAS exome

AF:

0.204

Gnomad4 FIN exome

AF:

0.0746

Gnomad4 NFE exome

AF:

0.0760

Gnomad4 OTH exome

AF:

0.107

GnomAD4 genome

AF:

0.108

AC:

16375

AN:

151268

Hom.:

1033

Cov.:

AF XY:

0.111

AC XY:

8179

AN XY:

73884

show subpopulations

Gnomad4 AFR

AF:

0.0957

Gnomad4 AMR

AF:

0.168

Gnomad4 ASJ

AF:

0.141

Gnomad4 EAS

AF:

0.244

Gnomad4 SAS

AF:

0.236

Gnomad4 FIN

AF:

0.0699

Gnomad4 NFE

AF:

0.0881

Gnomad4 OTH

AF:

0.108

Alfa

AF:

0.0273

Hom.:

Bravo

AF:

0.115

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over