NM_001366006.2:c.287+9603G>T

Variant names:

• chr1-81916833-G-T
• rs3790904
• NM_001366006.2:c.287+9603G>T

Variant summary

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

The NM_001366006.2(ADGRL2):​c.287+9603G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,644 control chromosomes in the GnomAD database, including 9,685 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 0.35 (9685 hom., cov: 31)
• Consequence: ADGRL2 NM_001366006.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 1 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366006.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRL2	NM_001366006.2	MANE Select	c.287+9603G>T		intron	N/A	NP_001352935.1
	ADGRL2	NM_001366005.2		c.287+9603G>T		intron	N/A	NP_001352934.1
	ADGRL2	NM_001350698.2		c.287+9603G>T		intron	N/A	NP_001337627.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRL2	ENST00000686636.1	MANE Select	c.287+9603G>T		intron	N/A	ENSP00000509478.1
	ADGRL2	ENST00000370725.5	TSL:5	c.287+9603G>T		intron	N/A	ENSP00000359760.1
	ADGRL2	ENST00000370723.5	TSL:5	c.287+9603G>T		intron	N/A	ENSP00000359758.1

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53432 AN: 151524 Hom.: 9678 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.353 AC: 53473 AN: 151644 Hom.: 9685 Cov.: 31 AF XY: 0.353 AC XY: 26185 AN XY: 74082

African (AFR) AF: 0.320 AC: 13245 AN: 41362

American (AMR) AF: 0.293 AC: 4462 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1243 AN: 3468

East Asian (EAS) AF: 0.256 AC: 1315 AN: 5146

South Asian (SAS) AF: 0.378 AC: 1812 AN: 4788

European-Finnish (FIN) AF: 0.425 AC: 4440 AN: 10450

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.376 AC: 25544 AN: 67912

Other (OTH) AF: 0.364 AC: 767 AN: 2106

Alfa AF: 0.360 Hom.: 1206

Bravo AF: 0.341

Asia WGS AF: 0.306 AC: 1054 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.46
PhyloP100		-0.027
Mutation Taster		=100/0	polymorphism (auto)

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: rs3790904; hg19: chr1-82382517;