chr1-46398839-G-A

Position:

• chr1-46398839-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001441.3(FAAH):​c.196-3252G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 152,040 control chromosomes in the GnomAD database, including 37,198 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 0.70 (37198 hom., cov: 32)
• Consequence: FAAH NM_001441.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAAH	NM_001441.3	c.196-3252G>A		intron_variant		ENST00000243167.9	NP_001432.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAAH	ENST00000243167.9	c.196-3252G>A		intron_variant		1	NM_001441.3	ENSP00000243167.8
FAAH	ENST00000468718.5	n.216-3252G>A		intron_variant		3
FAAH	ENST00000493735.5	n.174-3252G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105682 AN: 151922 Hom.: 37183 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.724

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.695 AC: 105742 AN: 152040 Hom.: 37198 Cov.: 32 AF XY: 0.696 AC XY: 51715 AN XY: 74322

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.814

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.702

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.715

Alfa AF: 0.695 Hom.: 4589

Bravo AF: 0.688

Asia WGS AF: 0.760 AC: 2641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.24
DANN	Benign	0.57

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

Other links and lift over

dbSNP: rs6429600; hg19: chr1-46864511;