chr4-61587491-A-G

Position:

• chr4-61587491-A-G

Variant summary

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

The NM_001387552.1(ADGRL3):​c.473+51A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 1,258,356 control chromosomes in the GnomAD database, including 59,011 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 0.34 (9523 hom., cov: 33)
  • Exomes 𝑓: 0.28 (49488 hom.)
• Consequence: ADGRL3 NM_001387552.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

Genes affected

ADGRL3 (HGNC:20974): (adhesion G protein-coupled receptor L3) This gene encodes a member of the latrophilin subfamily of G-protein coupled receptors (GPCR). Latrophilins may function in both cell adhesion and signal transduction. In experiments with non-human species, endogenous proteolytic cleavage within a cysteine-rich GPS (G-protein-coupled-receptor proteolysis site) domain resulted in two subunits (a large extracellular N-terminal cell adhesion subunit and a subunit with substantial similarity to the secretin/calcitonin family of GPCRs) being non-covalently bound at the cell membrane. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADGRL3	NM_001387552.1	c.473+51A>G		intron_variant		ENST00000683033.1	NP_001374481.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADGRL3	ENST00000683033.1	c.473+51A>G		intron_variant			NM_001387552.1	ENSP00000507980

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51277 AN: 151890 Hom.: 9506 Cov.: 33

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.320

GnomAD4 exome AF: 0.279 AC: 308973 AN: 1106348 Hom.: 49488 AF XY: 0.279 AC XY: 155981 AN XY: 558400

Gnomad4 AFR exome AF: 0.417

Gnomad4 AMR exome AF: 0.554

Gnomad4 ASJ exome AF: 0.251

Gnomad4 EAS exome AF: 0.619

Gnomad4 SAS exome AF: 0.340

Gnomad4 FIN exome AF: 0.320

Gnomad4 NFE exome AF: 0.239

Gnomad4 OTH exome AF: 0.296

GnomAD4 genome AF: 0.338 AC: 51333 AN: 152008 Hom.: 9523 Cov.: 33 AF XY: 0.347 AC XY: 25769 AN XY: 74294

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.323

Alfa AF: 0.280 Hom.: 7259

Bravo AF: 0.352

Asia WGS AF: 0.510 AC: 1768 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.0080
DANN	Benign	0.76

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: rs2172802; hg19: chr4-62453209; COSMIC: COSV72268273;