ENST00000655029.1:c.-338+40754C>T

Variant names:

• chr1-79195699-G-A
• rs228545
• ENST00000655029.1:c.-338+40754C>T

Variant summary

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

The ENST00000655029.1(ADGRL4):​c.-338+40754C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,976 control chromosomes in the GnomAD database, including 24,480 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 0.56 (24480 hom., cov: 32)
• Consequence: ADGRL4 ENST00000655029.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.375
• Publications: 2 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 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.-338+40754C>T		intron_variant	Intron 1 of 16			ENSP00000499618.1
ADGRL4	ENST00000661030.1	c.-337-82549C>T		intron_variant	Intron 1 of 16			ENSP00000499792.1
ADGRL4	ENST00000662895.1	n.-305+40754C>T		intron_variant	Intron 1 of 14			ENSP00000499579.1

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85277 AN: 151858 Hom.: 24434 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.562 AC: 85384 AN: 151976 Hom.: 24480 Cov.: 32 AF XY: 0.562 AC XY: 41761 AN XY: 74286

African (AFR) AF: 0.650 AC: 26952 AN: 41464

American (AMR) AF: 0.515 AC: 7857 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1726 AN: 3466

East Asian (EAS) AF: 0.821 AC: 4231 AN: 5156

South Asian (SAS) AF: 0.695 AC: 3346 AN: 4816

European-Finnish (FIN) AF: 0.463 AC: 4882 AN: 10554

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.511 AC: 34716 AN: 67950

Other (OTH) AF: 0.540 AC: 1139 AN: 2108

Alfa AF: 0.530 Hom.: 2698

Bravo AF: 0.568

Asia WGS AF: 0.760 AC: 2642 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.2
DANN	Benign	0.29
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs228545; hg19: chr1-79661384;