rs6703669

Variant names:

• chr1-46396883-C-T
• rs6703669
• NM_001441.3:c.195+2340C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001441.3(FAAH):​c.195+2340C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,202 control chromosomes in the GnomAD database, including 4,305 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 0.22 (4305 hom., cov: 33)
• Consequence: FAAH NM_001441.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.801
• Publications: 15 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001441.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAAH	NM_001441.3	MANE Select	c.195+2340C>T		intron	N/A	NP_001432.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAAH	ENST00000243167.9	TSL:1 MANE Select	c.195+2340C>T		intron	N/A	ENSP00000243167.8
	FAAH	ENST00000877148.1		c.195+2340C>T		intron	N/A	ENSP00000547207.1
	FAAH	ENST00000877151.1		c.195+2340C>T		intron	N/A	ENSP00000547210.1

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34153 AN: 152084 Hom.: 4305 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0206

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.224 AC: 34148 AN: 152202 Hom.: 4305 Cov.: 33 AF XY: 0.220 AC XY: 16369 AN XY: 74408

African (AFR) AF: 0.149 AC: 6186 AN: 41538

American (AMR) AF: 0.187 AC: 2860 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 654 AN: 3472

East Asian (EAS) AF: 0.0208 AC: 108 AN: 5192

South Asian (SAS) AF: 0.108 AC: 522 AN: 4828

European-Finnish (FIN) AF: 0.311 AC: 3291 AN: 10584

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19779 AN: 67984

Other (OTH) AF: 0.219 AC: 463 AN: 2112

Alfa AF: 0.243 Hom.: 787

Bravo AF: 0.215

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.73
PhyloP100		0.80
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6703669; hg19: chr1-46862555;