chr1-46408231-C-T

Position:

• chr1-46408231-C-T

Variant summary

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

The NM_001441.3(FAAH):​c.952-228C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0556 in 152,206 control chromosomes in the GnomAD database, including 612 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 0.056 (612 hom., cov: 32)
• Consequence: FAAH NM_001441.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAAH	NM_001441.3	c.952-228C>T		intron_variant		ENST00000243167.9	NP_001432.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAAH	ENST00000243167.9	c.952-228C>T		intron_variant		1	NM_001441.3	ENSP00000243167.8
FAAH	ENST00000484697.5	n.72-228C>T		intron_variant		1		ENSP00000481641.1
FAAH	ENST00000489366.2	n.167-228C>T		intron_variant		3
FAAH	ENST00000493735.5	n.1173-228C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0557 AC: 8465 AN: 152088 Hom.: 611 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.0434

Gnomad ASJ AF: 0.00403

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.0133

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00663

Gnomad OTH AF: 0.0465

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

GnomAD4 genome AF: 0.0556 AC: 8464 AN: 152206 Hom.: 612 Cov.: 32 AF XY: 0.0599 AC XY: 4454 AN XY: 74404

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.0434

Gnomad4 ASJ AF: 0.00403

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.0133

Gnomad4 NFE AF: 0.00662

Gnomad4 OTH AF: 0.0475

Alfa AF: 0.0293 Hom.: 19

Bravo AF: 0.0588

Asia WGS AF: 0.239 AC: 831 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.1
DANN	Benign	0.47

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: rs873978; hg19: chr1-46873903; COSMIC: COSV54545380; COSMIC: COSV54545380;