rs6687262

chr1-79043424-T-C

Variant summary

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

The ENST00000655029.1(ADGRL4):c.-113-38205A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 152,164 control chromosomes in the GnomAD database, including 18,534 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 0.47 (18534 hom., cov: 33)
• Consequence: ADGRL4 ENST00000655029.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

Genes affected

ADGRL4 (HGNC:20822): (adhesion G protein-coupled receptor L4) Predicted to enable G protein-coupled receptor activity. Predicted to be involved in adenylate cyclase-activating G protein-coupled receptor signaling pathway. Predicted to be located in cytoplasmic vesicle and plasma membrane. Predicted to be integral component of plasma membrane. Biomarker of glioblastoma and hypertrophic cardiomyopathy. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADGRL4	ENST00000655029.1	c.-113-38205A>G		intron_variant
ADGRL4	ENST00000656300.1	c.-80-96998A>G		intron_variant
ADGRL4	ENST00000661030.1	c.-113-38205A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71437 AN: 152048 Hom.: 18529 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.470 AC: 71471 AN: 152164 Hom.: 18534 Cov.: 33 AF XY: 0.466 AC XY: 34670 AN XY: 74382

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.507

Alfa AF: 0.574 Hom.: 51287

Bravo AF: 0.461

Asia WGS AF: 0.526 AC: 1825 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	4.7
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6687262; hg19: chr1-79509109;