Genetic Variant NM_001441.3:c.822G>A (chr1-46406074-G-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001441.3(FAAH):c.822G>A(p.Glu274Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0439 in 1,614,138 control chromosomes in the GnomAD database, including 1,855 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.032 ( 120 hom., cov: 33)

Exomes 𝑓: 0.045 ( 1735 hom. )

Consequence

FAAH
NM_001441.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.157

Publications

4 publications found

Variant links:

Genes affected

FAAH (HGNC:3553): (fatty acid amide hydrolase) This gene encodes a protein that is responsible for the hydrolysis of a number of primary and secondary fatty acid amides, including the neuromodulatory compounds anandamide and oleamide. [provided by RefSeq, Jul 2008]

FAAH links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAAH	NM_001441.3 link	c.822G>A	p.Glu274Glu	synonymous_variant	Exon 6 of 15	ENST00000243167.9	NP_001432.2	O00519Q9UG55

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
FAAH	ENST00000243167.9 link	c.822G>A	p.Glu274Glu	synonymous_variant	Exon 6 of 15	1	NM_001441.3	ENSP00000243167.8	O00519
FAAH	ENST00000484697.5 link	n.71+280G>A		intron_variant	Intron 1 of 7	1		ENSP00000481641.1	A0A087WYA0
FAAH	ENST00000489366.2 link	n.37G>A		non_coding_transcript_exon_variant	Exon 1 of 4	3
FAAH	ENST00000493735.5 link	n.1043G>A		non_coding_transcript_exon_variant	Exon 5 of 8	5

Frequencies

GnomAD3 genomes

AF:

0.0316

AC:

4802

AN:

152198

Hom.:

120

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00837

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0258

Gnomad ASJ

AF:

0.0173

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0141

Gnomad FIN

AF:

0.0632

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0470

Gnomad OTH

AF:

0.0267

GnomAD2 exomes

AF:

0.0325

AC:

8168

AN:

251372

AF XY:

0.0329

show subpopulations

Gnomad AFR exome

AF:

0.00775

Gnomad AMR exome

AF:

0.0127

Gnomad ASJ exome

AF:

0.0180

Gnomad EAS exome

AF:

0.000109

Gnomad FIN exome

AF:

0.0687

Gnomad NFE exome

AF:

0.0462

Gnomad OTH exome

AF:

0.0318

GnomAD4 exome

AF:

0.0452

AC:

66119

AN:

1461822

Hom.:

1735

Cov.:

AF XY:

0.0446

AC XY:

32467

AN XY:

727202

show subpopulations

African (AFR)

AF:

0.00705

AC:

236

AN:

33480

American (AMR)

AF:

0.0136

AC:

610

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0190

AC:

496

AN:

26136

East Asian (EAS)

AF:

0.0000252

AC:

AN:

39700

South Asian (SAS)

AF:

0.0166

AC:

1430

AN:

86256

European-Finnish (FIN)

AF:

0.0673

AC:

3591

AN:

53388

Middle Eastern (MID)

AF:

0.00537

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.0516

AC:

57367

AN:

1111976

Other (OTH)

AF:

0.0390

AC:

2357

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

3816

7632

11449

15265

19081

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2110

4220

6330

8440

10550

<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:

0.0315

AC:

4800

AN:

152316

Hom.:

120

Cov.:

AF XY:

0.0321

AC XY:

2391

AN XY:

74476

show subpopulations

African (AFR)

AF:

0.00835

AC:

347

AN:

41570

American (AMR)

AF:

0.0258

AC:

395

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.0173

AC:

AN:

3470

East Asian (EAS)

AF:

0.000386

AC:

AN:

5182

South Asian (SAS)

AF:

0.0141

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.0632

AC:

671

AN:

10614

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0469

AC:

3193

AN:

68016

Other (OTH)

AF:

0.0265

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

244

488

731

975

1219

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

180

240

300

<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:

0.0393

Hom.:

111

Bravo

AF:

0.0284

Asia WGS

AF:

0.00693

AC:

AN:

3478

EpiCase

AF:

0.0414

EpiControl

AF:

0.0424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

(source)

DANN

Benign

0.40

PhyloP100

0.16

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.22

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.22

Position offset: -36

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