NM_001387552.1:c.1399+16908A>G

Variant names:

• chr4-61750462-A-G
• rs12646895
• NM_001387552.1:c.1399+16908A>G

Variant summary

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

The NM_001387552.1(ADGRL3):​c.1399+16908A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 152,014 control chromosomes in the GnomAD database, including 27,574 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 0.57 (27574 hom., cov: 32)
• Consequence: ADGRL3 NM_001387552.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386
• Publications: 3 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]

ENSG00000289308 (HGNC:58799):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001387552.1. 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
	ADGRL3	NM_001387552.1	MANE Select	c.1399+16908A>G		intron	N/A	NP_001374481.1
	ADGRL3	NM_001322402.3		c.1399+16908A>G		intron	N/A	NP_001309331.1
	ADGRL3	NM_001371344.2		c.1399+16908A>G		intron	N/A	NP_001358273.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRL3	ENST00000683033.1	MANE Select	c.1399+16908A>G		intron	N/A	ENSP00000507980.1
	ADGRL3	ENST00000512091.6	TSL:1	c.1195+16908A>G		intron	N/A	ENSP00000423388.1
	ENSG00000289308	ENST00000692606.2		n.952T>C		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87232 AN: 151896 Hom.: 27505 Cov.: 32

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.575 AC: 87363 AN: 152014 Hom.: 27574 Cov.: 32 AF XY: 0.578 AC XY: 42976 AN XY: 74294

African (AFR) AF: 0.824 AC: 34168 AN: 41468

American (AMR) AF: 0.637 AC: 9726 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1641 AN: 3470

East Asian (EAS) AF: 0.814 AC: 4198 AN: 5158

South Asian (SAS) AF: 0.498 AC: 2401 AN: 4826

European-Finnish (FIN) AF: 0.506 AC: 5336 AN: 10544

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.415 AC: 28186 AN: 67958

Other (OTH) AF: 0.567 AC: 1197 AN: 2110

Alfa AF: 0.465 Hom.: 62622

Bravo AF: 0.600

Asia WGS AF: 0.670 AC: 2329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.77
PhyloP100		-0.39
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: rs12646895; hg19: chr4-62616180;