Variant rs6661174 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.1414C>T(p.Gln472Ter) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.992 in 1,613,588 control chromosomes in the GnomAD database, including 794,999 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.96 ( 70946 hom., cov: 31)

Exomes 𝑓: 1.0 ( 724053 hom. )

Consequence

FMO2
NM_001460.5 stop_gained

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 7.91

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 1-171208951-C-T is Benign according to our data. Variant chr1-171208951-C-T is described in ClinVar as [Benign]. Clinvar id is 769222.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
FMO2	NM_001460.5 linkuse as main transcript	c.1414C>T	p.Gln472Ter	stop_gained	9/9	ENST00000209929.10	NP_001451.2
LOC124900413	XR_007066731.1 linkuse as main transcript	n.366-12013G>A		intron_variant, non_coding_transcript_variant
LOC105371611	XR_922278.4 linkuse as main transcript	n.514+38630G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
FMO2	ENST00000209929.10 linkuse as main transcript	c.1414C>T	p.Gln472Ter	stop_gained	9/9	1	NM_001460.5	ENSP00000209929	P1
	ENST00000445290.1 linkuse as main transcript	n.139-9436G>A		intron_variant, non_coding_transcript_variant		2
	ENST00000669750.1 linkuse as main transcript	n.448+38615G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.964

AC:

146637

AN:

152068

Hom.:

70918

Cov.:

show subpopulations

Gnomad AFR

AF:

0.879

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.985

Gnomad ASJ

AF:

1.00

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.989

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.981

Gnomad NFE

AF:

0.999

Gnomad OTH

AF:

0.974

GnomAD4 exome

AF:

0.995

AC:

1454424

AN:

1461402

Hom.:

724053

Cov.:

AF XY:

0.995

AC XY:

723575

AN XY:

726990

show subpopulations

Gnomad4 AFR exome

AF:

0.875

Gnomad4 AMR exome

AF:

0.992

Gnomad4 ASJ exome

AF:

1.00

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.989

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.999

Gnomad4 OTH exome

AF:

0.989

GnomAD4 genome

AF:

0.964

AC:

146712

AN:

152186

Hom.:

70946

Cov.:

AF XY:

0.965

AC XY:

71793

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.878

Gnomad4 AMR

AF:

0.985

Gnomad4 ASJ

AF:

1.00

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.989

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

0.999

Gnomad4 OTH

AF:

0.974

Alfa

AF:

0.992

Hom.:

174166

Bravo

AF:

0.960

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

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.31

CADD

Pathogenic

Vest4

0.56

Splicing

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