1-81915802-G-A

Position:

• chr1-81915802-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.287+8572G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0528 in 152,160 control chromosomes in the GnomAD database, including 597 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 0.053 (597 hom., cov: 32)
• Consequence: ADGRL2 NM_001366006.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397

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]

ADGRL2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADGRL2	NM_001366006.2	c.287+8572G>A		intron_variant		ENST00000686636.1	NP_001352935.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADGRL2	ENST00000686636.1	c.287+8572G>A		intron_variant			NM_001366006.2	ENSP00000509478.1
ADGRL2	ENST00000370725.5	c.287+8572G>A		intron_variant		5		ENSP00000359760.1
ADGRL2	ENST00000370723.5	c.287+8572G>A		intron_variant		5		ENSP00000359758.1
ADGRL2	ENST00000370728.5	c.287+8572G>A		intron_variant		5		ENSP00000359763.1
ADGRL2	ENST00000370727.5	c.287+8572G>A		intron_variant		5		ENSP00000359762.1
ADGRL2	ENST00000370730.5	c.287+8572G>A		intron_variant		5		ENSP00000359765.1
ADGRL2	ENST00000370721.5	c.287+8572G>A		intron_variant		5		ENSP00000359756.1

Frequencies

GnomAD3 genomes AF: 0.0528 AC: 8027 AN: 152042 Hom.: 597 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0198

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.0346

Gnomad SAS AF: 0.0566

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00526

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0528 AC: 8041 AN: 152160 Hom.: 597 Cov.: 32 AF XY: 0.0518 AC XY: 3851 AN XY: 74386

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.0197

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.0348

Gnomad4 SAS AF: 0.0572

Gnomad4 FIN AF: 0.000189

Gnomad4 NFE AF: 0.00526

Gnomad4 OTH AF: 0.0435

Alfa AF: 0.0345 Hom.: 65

Bravo AF: 0.0583

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.65

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: rs648392; hg19: chr1-82381486;