rs2015312

Variant names:

• chrX-57392766-C-G
• rs2015312
• NM_174912.4:c.996+11737C>G

Your query was ambiguous. Multiple possible variants found:

• chrX-57392766-C-G
• chrX-57392766-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_174912.4(FAAH2):​c.996+11737C>G variant causes a intron change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 23)
  • Exomes 𝑓: 0.0000040 (0 hom. 1 hem.)
  • Failed GnomAD Quality Control
• Consequence: FAAH2 NM_174912.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.55
• Publications: 4 publications found

Genes affected

FAAH2 (HGNC:26440): (fatty acid amide hydrolase 2) This gene encodes a fatty acid amide hydrolase that shares a conserved protein motif with the amidase signature family of enzymes. The encoded enzyme is able to catalyze the hydrolysis of a broad range of bioactive lipids, including those from the three main classes of fatty acid amides; N-acylethanolamines, fatty acid primary amides and N-acyl amino acids. This enzyme has a preference for monounsaturated acyl chains as a substrate. Alternate splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2017]

MTHFD1P1 (HGNC:7433): (methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 pseudogene 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAAH2	NM_174912.4	c.996+11737C>G		intron_variant	Intron 7 of 10	ENST00000374900.5	NP_777572.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAAH2	ENST00000374900.5	c.996+11737C>G		intron_variant	Intron 7 of 10	1	NM_174912.4	ENSP00000364035.4
MTHFD1P1	ENST00000413059.1	n.2644G>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000400 AC: 2 AN: 500479 Hom.: 0 Cov.: 7 AF XY: 0.00000576 AC XY: 1 AN XY: 173485

African (AFR) AF: 0.00 AC: 0 AN: 14760

American (AMR) AF: 0.0000587 AC: 2 AN: 34050

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15362

East Asian (EAS) AF: 0.00 AC: 0 AN: 27249

South Asian (SAS) AF: 0.00 AC: 0 AN: 42573

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38655

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3036

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 298854

Other (OTH) AF: 0.00 AC: 0 AN: 25940

GnomAD4 genome Cov.: 23

Alfa AF: 0.00 Hom.: 1242

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	11
DANN	Benign	0.68
PhyloP100		5.5

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: rs2015312; hg19: chrX-57419199;