1-79255438-C-T

Variant names:

• chr1-79255438-C-T
• rs6674681
• ENST00000661030.1:c.-338+26484G>A

Variant summary

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

The ENST00000661030.1(ADGRL4):​c.-338+26484G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 152,072 control chromosomes in the GnomAD database, including 16,520 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 0.41 (16520 hom., cov: 32)
• Consequence: ADGRL4 ENST00000661030.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.754 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	ENST00000661030.1	c.-338+26484G>A		intron_variant	Intron 1 of 16			ENSP00000499792.1

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62176 AN: 151954 Hom.: 16480 Cov.: 32

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.410 AC: 62276 AN: 152072 Hom.: 16520 Cov.: 32 AF XY: 0.406 AC XY: 30154 AN XY: 74342

African (AFR) AF: 0.761 AC: 31560 AN: 41476

American (AMR) AF: 0.320 AC: 4892 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1026 AN: 3466

East Asian (EAS) AF: 0.426 AC: 2198 AN: 5162

South Asian (SAS) AF: 0.353 AC: 1705 AN: 4824

European-Finnish (FIN) AF: 0.224 AC: 2367 AN: 10586

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17537 AN: 67972

Other (OTH) AF: 0.375 AC: 792 AN: 2114

Alfa AF: 0.309 Hom.: 22253

Bravo AF: 0.429

Asia WGS AF: 0.409 AC: 1427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.48
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs6674681; hg19: chr1-79721123;