rs6687262

Variant names:

• chr1-79043424-T-C
• rs6687262
• ENST00000655029.1:c.-113-38205A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRL4	ENST00000655029.1	c.-113-38205A>G		intron_variant	Intron 3 of 16			ENSP00000499618.1
ADGRL4	ENST00000661030.1	c.-113-38205A>G		intron_variant	Intron 3 of 16			ENSP00000499792.1
ADGRL4	ENST00000656300.1	c.-80-96998A>G		intron_variant	Intron 1 of 4			ENSP00000499265.1

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

African (AFR) AF: 0.237 AC: 9856 AN: 41516

American (AMR) AF: 0.467 AC: 7151 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2122 AN: 3472

East Asian (EAS) AF: 0.507 AC: 2623 AN: 5178

South Asian (SAS) AF: 0.558 AC: 2693 AN: 4828

European-Finnish (FIN) AF: 0.483 AC: 5105 AN: 10570

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40120 AN: 67992

Other (OTH) AF: 0.507 AC: 1069 AN: 2108

Alfa AF: 0.561 Hom.: 99135

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
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs6687262; hg19: chr1-79509109;