XR_001740896.2:n.716C>A

Variant names:

• chr3-127832787-G-T
• rs11716997
• XR_001740896.2:n.716C>A

Variant summary

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

The XR_001740896.2(LOC107986129):​n.716C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,084 control chromosomes in the GnomAD database, including 29,037 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 0.61 (29037 hom., cov: 32)
• Consequence: LOC107986129 XR_001740896.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870
• Publications: 11 publications found

Genes affected

LOC107986129 (HGNC:):

MGLL (HGNC:17038): (monoglyceride lipase) This gene encodes a serine hydrolase of the AB hydrolase superfamily that catalyzes the conversion of monoacylglycerides to free fatty acids and glycerol. The encoded protein plays a critical role in several physiological processes including pain and nociperception through hydrolysis of the endocannabinoid 2-arachidonoylglycerol. Expression of this gene may play a role in cancer tumorigenesis and metastasis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986129	XR_001740896.2	n.716C>A		non_coding_transcript_exon_variant	Exon 5 of 5
LOC107986129	XR_001740898.2	n.623C>A		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGLL	ENST00000648300.1	n.-1102-1742C>A		intron_variant	Intron 3 of 12			ENSP00000497905.1
ENSG00000287143	ENST00000785485.1	n.145-4639G>T		intron_variant	Intron 1 of 3
ENSG00000302312	ENST00000785719.1	n.168-785G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93229 AN: 151966 Hom.: 29017 Cov.: 32

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.613 AC: 93296 AN: 152084 Hom.: 29037 Cov.: 32 AF XY: 0.613 AC XY: 45564 AN XY: 74330

African (AFR) AF: 0.718 AC: 29802 AN: 41496

American (AMR) AF: 0.546 AC: 8348 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2179 AN: 3470

East Asian (EAS) AF: 0.500 AC: 2581 AN: 5166

South Asian (SAS) AF: 0.723 AC: 3486 AN: 4820

European-Finnish (FIN) AF: 0.561 AC: 5923 AN: 10562

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38873 AN: 67972

Other (OTH) AF: 0.585 AC: 1235 AN: 2112

Alfa AF: 0.576 Hom.: 42177

Bravo AF: 0.611

Asia WGS AF: 0.628 AC: 2183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.49
PhyloP100		0.087

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11716997; hg19: chr3-127551630; COSMIC: COSV60111780;