rs11163372

Positions:

• chr1-81781563-C-T

Variant summary

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

The ENST00000359929.7(ADGRL2):​c.-101+19711C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,068 control chromosomes in the GnomAD database, including 3,153 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 0.20 (3153 hom., cov: 32)
• Consequence: ADGRL2 ENST00000359929.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADGRL2	NM_001297704.3	c.-101+19711C>T		intron_variant			NP_001284633.1
ADGRL2	NM_001366003.2	c.-101+19711C>T		intron_variant			NP_001352932.1
ADGRL2	NM_001366004.2	c.-101+19711C>T		intron_variant			NP_001352933.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADGRL2	ENST00000359929.7	c.-101+19711C>T		intron_variant		1		ENSP00000353006
ADGRL2	ENST00000370721.5	c.-101+19711C>T		intron_variant		5		ENSP00000359756
ADGRL2	ENST00000370723.5	c.-101+19711C>T		intron_variant		5		ENSP00000359758

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29721 AN: 151950 Hom.: 3151 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0784

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.196 AC: 29748 AN: 152068 Hom.: 3153 Cov.: 32 AF XY: 0.198 AC XY: 14685 AN XY: 74334

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.0782

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.165

Alfa AF: 0.170 Hom.: 1886

Bravo AF: 0.197

Asia WGS AF: 0.129 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.29

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: rs11163372; hg19: chr1-82247248;