1-79092119-C-T

Variant names:

• chr1-79092119-C-T
• rs1332836
• ENST00000655029.1:c.-114+3364G>A

Variant summary

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

The ENST00000655029.1(ADGRL4):​c.-114+3364G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 151,826 control chromosomes in the GnomAD database, including 2,662 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 0.18 (2662 hom., cov: 32)
• Consequence: ADGRL4 ENST00000655029.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.256 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.-114+3364G>A		intron_variant	Intron 3 of 16			ENSP00000499618.1
ADGRL4	ENST00000661030.1	c.-114+3364G>A		intron_variant	Intron 3 of 16			ENSP00000499792.1
ADGRL4	ENST00000656300.1	c.-81+96224G>A		intron_variant	Intron 1 of 4			ENSP00000499265.1

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27481 AN: 151708 Hom.: 2657 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.181 AC: 27501 AN: 151826 Hom.: 2662 Cov.: 32 AF XY: 0.185 AC XY: 13726 AN XY: 74150

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.180

Alfa AF: 0.155 Hom.: 1209

Bravo AF: 0.177

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.20
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1332836; hg19: chr1-79557804;