rs3790889

chr1-81946916-G-A

Variant summary

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

The NM_001366006.2(ADGRL2):c.1210+3147G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,930 control chromosomes in the GnomAD database, including 11,409 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 0.38 (11409 hom., cov: 31)
• Consequence: ADGRL2 NM_001366006.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257

Genes affected

ADGRL2 (HGNC:18582): (adhesion G protein-coupled receptor L2) This gene encodes a member of the latrophilin subfamily of G-protein coupled receptors. The encoded protein participates in the regulation of exocytosis. The proprotein is thought to be further cleaved within a cysteine-rich G-protein-coupled receptor proteolysis site into two chains that are non-covalently bound at the cell membrane. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADGRL2	NM_001366006.2	c.1210+3147G>A		intron_variant		ENST00000686636.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADGRL2	ENST00000686636.1	c.1210+3147G>A		intron_variant			NM_001366006.2

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57927 AN: 151812 Hom.: 11399 Cov.: 31

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.382 AC: 57972 AN: 151930 Hom.: 11409 Cov.: 31 AF XY: 0.381 AC XY: 28253 AN XY: 74234

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.388

Alfa AF: 0.398 Hom.: 6574

Bravo AF: 0.371

Asia WGS AF: 0.318 AC: 1108 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.64

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: rs3790889; hg19: chr1-82412600;