rs324420
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001441(FAAH):c.385C>A(p.Pro129Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152014 control chromosomes in the gnomAD Genomes database, including 5570 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.26 ( 5570 hom., cov: 33)
Exomes 𝑓: 0.24 ( 7639 hom. )
Consequence
FAAH
NM_001441 missense
NM_001441 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: -0.386
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0037901402).
BP6
?
Variant 1:46405089-C>A is Benign according to our data. Variant chr1-46405089-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 6724. Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAAH | NM_001441.3 | c.385C>A | p.Pro129Thr | missense_variant | 3/15 | ENST00000243167.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAAH | ENST00000243167.9 | c.385C>A | p.Pro129Thr | missense_variant | 3/15 | 1 | NM_001441.3 | P1 | |
FAAH | ENST00000468718.5 | n.405C>A | non_coding_transcript_exon_variant | 3/5 | 3 | ||||
FAAH | ENST00000493735.5 | n.363C>A | non_coding_transcript_exon_variant | 3/8 | 5 |
Frequencies
GnomAD3 genomes AF: 0.260 AC: 39514AN: 152014Hom.: 5570 Cov.: 33
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GnomAD3 exomes AF: 0.236 AC: 59345AN: 251362Hom.: 7639 AF XY: 0.225 AC XY: 30632AN XY: 135898
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GnomAD4 exome AF: 0.215 AC: 314560AN: 1461644Hom.: 35488 AF XY: 0.214 AC XY: 155434AN XY: 727132
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ALSPAC
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731
ESP6500AA
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1533
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1722
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Polysubstance abuse, susceptibility to Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 08, 2021 | - - |
FAAH POLYMORPHISM Benign:1
Benign, no assertion criteria provided | literature only | OMIM | Apr 01, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
P
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at