rs324418

chr1-46407026-A-G

Variant summary

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

The NM_001441.3(FAAH):c.951+658A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,578 control chromosomes in the GnomAD database, including 6,495 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 0.28 (6495 hom., cov: 30)
• Consequence: FAAH NM_001441.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.232

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAAH	NM_001441.3	c.951+658A>G		intron_variant		ENST00000243167.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAAH	ENST00000243167.9	c.951+658A>G		intron_variant		1	NM_001441.3	P1
FAAH	ENST00000484697.5	c.72+1232A>G		intron_variant, NMD_transcript_variant		1
FAAH	ENST00000489366.2	n.166+658A>G		intron_variant, non_coding_transcript_variant		3
FAAH	ENST00000493735.5	n.1172+658A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42847 AN: 151464 Hom.: 6488 Cov.: 30

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.283 AC: 42886 AN: 151578 Hom.: 6495 Cov.: 30 AF XY: 0.286 AC XY: 21167 AN XY: 74056

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.255

Alfa AF: 0.285 Hom.: 1134

Bravo AF: 0.285

Asia WGS AF: 0.204 AC: 711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.1
Dann	Benign	0.62

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: rs324418; hg19: chr1-46872698;