rs11576941

chr1-46409395-G-T

Variant summary

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

The NM_001441.3(FAAH):c.1175+197G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 598,906 control chromosomes in the GnomAD database, including 29,125 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 0.27 (6375 hom., cov: 31)
  • Exomes 𝑓: 0.31 (22750 hom.)
• Consequence: FAAH NM_001441.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.552

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAAH	NM_001441.3	c.1175+197G>T		intron_variant		ENST00000243167.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAAH	ENST00000243167.9	c.1175+197G>T		intron_variant		1	NM_001441.3	P1
FAAH	ENST00000484697.5	c.*148+197G>T		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41610 AN: 151624 Hom.: 6380 Cov.: 31

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.299

GnomAD4 exome AF: 0.310 AC: 138832 AN: 447162 Hom.: 22750 AF XY: 0.305 AC XY: 73689 AN XY: 241310

Gnomad4 AFR exome AF: 0.158

Gnomad4 AMR exome AF: 0.387

Gnomad4 ASJ exome AF: 0.446

Gnomad4 EAS exome AF: 0.472

Gnomad4 SAS exome AF: 0.226

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.308

Gnomad4 OTH exome AF: 0.324

GnomAD4 genome AF: 0.274 AC: 41599 AN: 151744 Hom.: 6375 Cov.: 31 AF XY: 0.273 AC XY: 20270 AN XY: 74124

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.295

Alfa AF: 0.311 Hom.: 12673

Bravo AF: 0.279

Asia WGS AF: 0.367 AC: 1272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.0
Dann	Benign	0.79

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: rs11576941; hg19: chr1-46875067; COSMIC: COSV54543518; COSMIC: COSV54543518;