rs1456873

Variant names:

• chr4-61436445-G-A
• rs1456873
• NM_001387552.1:c.-174+53256G>A

Variant summary

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

The NM_001387552.1(ADGRL3):​c.-174+53256G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 152,000 control chromosomes in the GnomAD database, including 12,307 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 0.39 (12307 hom., cov: 33)
• Consequence: ADGRL3 NM_001387552.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• Publications: 4 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRL3	NM_001387552.1	c.-174+53256G>A		intron_variant	Intron 2 of 26	ENST00000683033.1	NP_001374481.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRL3	ENST00000683033.1	c.-174+53256G>A		intron_variant	Intron 2 of 26		NM_001387552.1	ENSP00000507980.1
ADGRL3	ENST00000512091.6	c.-174+53256G>A		intron_variant	Intron 2 of 25	1		ENSP00000423388.1
ADGRL3	ENST00000514591.5	c.-174+53256G>A		intron_variant	Intron 2 of 24	5		ENSP00000422533.1

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59794 AN: 151880 Hom.: 12302 Cov.: 33

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.393 AC: 59808 AN: 152000 Hom.: 12307 Cov.: 33 AF XY: 0.395 AC XY: 29373 AN XY: 74296

African (AFR) AF: 0.293 AC: 12144 AN: 41454

American (AMR) AF: 0.397 AC: 6065 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1400 AN: 3468

East Asian (EAS) AF: 0.160 AC: 829 AN: 5178

South Asian (SAS) AF: 0.462 AC: 2228 AN: 4824

European-Finnish (FIN) AF: 0.463 AC: 4883 AN: 10554

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30988 AN: 67934

Other (OTH) AF: 0.399 AC: 842 AN: 2112

Alfa AF: 0.421 Hom.: 2232

Bravo AF: 0.379

Asia WGS AF: 0.384 AC: 1334 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	9.1
DANN	Benign	0.90
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1456873; hg19: chr4-62302163;