dbSNP rs1736565: FMO6P:n.313C>T (chr1-171143351-C-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 4P and 8B. PP3_StrongBA1

The ENST00000236166.5(FMO6P):n.313C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 453,950 control chromosomes in the GnomAD database, including 78,501 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.61 ( 28735 hom., cov: 32)

Exomes 𝑓: 0.57 ( 49766 hom. )

Consequence

FMO6P
ENST00000236166.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.763

Publications

22 publications found

Variant links:

Genes affected

FMO6P (HGNC:24024): (flavin containing dimethylaniline monoxygenase 6, pseudogene) Predicted to enable monooxygenase activity. Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

FMO6P links:

FMO6P (HGNC:):

FMO6P links:

ENSG00000231424 (HGNC:40240):

ENSG00000231424 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

PP3

BayesDel_noAF computational evidence supports a deleterious effect, 0.65

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
FMO6P	NR_002601.1 link	n.906-3127C>T	intron_variant	Intron 1 of 6
FMO1-AS1	XR_001738291.3 link	n.600-21488G>A	intron_variant	Intron 3 of 3
FMO1-AS1	XR_922278.4 link	n.600-21488G>A	intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
FMO6P	ENST00000236166.5 link	n.313C>T	non_coding_transcript_exon_variant	Exon 2 of 8	6
FMO6P	ENST00000639860.1 link	n.422C>T	non_coding_transcript_exon_variant	Exon 2 of 3	5
FMO6P	ENST00000367754.3 link	n.906-3127C>T	intron_variant	Intron 1 of 6	2

Frequencies

GnomAD3 genomes

AF:

0.606

AC:

92034

AN:

151914

Hom.:

28677

Cov.:

show subpopulations

Gnomad AFR

AF:

0.767

Gnomad AMI

AF:

0.385

Gnomad AMR

AF:

0.611

Gnomad ASJ

AF:

0.512

Gnomad EAS

AF:

0.585

Gnomad SAS

AF:

0.623

Gnomad FIN

AF:

0.526

Gnomad MID

AF:

0.490

Gnomad NFE

AF:

0.529

Gnomad OTH

AF:

0.562

GnomAD2 exomes

AF:

0.584

AC:

77774

AN:

133268

AF XY:

0.578

show subpopulations

Gnomad AFR exome

AF:

0.771

Gnomad AMR exome

AF:

0.677

Gnomad ASJ exome

AF:

0.507

Gnomad EAS exome

AF:

0.595

Gnomad FIN exome

AF:

0.535

Gnomad NFE exome

AF:

0.528

Gnomad OTH exome

AF:

0.524

GnomAD4 exome

AF:

0.569

AC:

171829

AN:

301918

Hom.:

49766

Cov.:

AF XY:

0.569

AC XY:

97922

AN XY:

171966

show subpopulations

African (AFR)

AF:

0.765

AC:

6491

AN:

8480

American (AMR)

AF:

0.677

AC:

18243

AN:

26940

Ashkenazi Jewish (ASJ)

AF:

0.504

AC:

5389

AN:

10682

East Asian (EAS)

AF:

0.589

AC:

5377

AN:

9130

South Asian (SAS)

AF:

0.610

AC:

36072

AN:

59132

European-Finnish (FIN)

AF:

0.542

AC:

6872

AN:

12672

Middle Eastern (MID)

AF:

0.510

AC:

1411

AN:

2768

European-Non Finnish (NFE)

AF:

0.533

AC:

84227

AN:

157998

Other (OTH)

AF:

0.549

AC:

7747

AN:

14116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

3525

7050

10575

14100

17625

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

550

1100

1650

2200

2750

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.606

AC:

92151

AN:

152032

Hom.:

28735

Cov.:

AF XY:

0.606

AC XY:

45012

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.767

AC:

31830

AN:

41488

American (AMR)

AF:

0.612

AC:

9348

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.512

AC:

1774

AN:

3468

East Asian (EAS)

AF:

0.585

AC:

3023

AN:

5170

South Asian (SAS)

AF:

0.623

AC:

3001

AN:

4818

European-Finnish (FIN)

AF:

0.526

AC:

5546

AN:

10536

Middle Eastern (MID)

AF:

0.473

AC:

138

AN:

292

European-Non Finnish (NFE)

AF:

0.529

AC:

35957

AN:

67966

Other (OTH)

AF:

0.562

AC:

1183

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1848

3695

5543

7390

9238

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

766

1532

2298

3064

3830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.553

Hom.:

73134

Bravo

AF:

0.617

Asia WGS

AF:

0.596

AC:

2072

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Pathogenic

0.65

CADD

Benign

8.4

(source)

DANN

Uncertain

1.0

PhyloP100

0.76

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over