chr1-78910197-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_022159.4(ADGRL4):​c.1749+7437G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,582 control chromosomes in the GnomAD database, including 6,198 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 0.28 ( 6198 hom., cov: 33)

Consequence

ADGRL4
NM_022159.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.599
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ADGRL4NM_022159.4 linkuse as main transcriptc.1749+7437G>C intron_variant ENST00000370742.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ADGRL4ENST00000370742.4 linkuse as main transcriptc.1749+7437G>C intron_variant 1 NM_022159.4 P1

Frequencies

GnomAD3 genomes
AF:
0.285
AC:
43125
AN:
151464
Hom.:
6195
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.276
Gnomad AMI
AF:
0.454
Gnomad AMR
AF:
0.262
Gnomad ASJ
AF:
0.337
Gnomad EAS
AF:
0.236
Gnomad SAS
AF:
0.225
Gnomad FIN
AF:
0.276
Gnomad MID
AF:
0.320
Gnomad NFE
AF:
0.299
Gnomad OTH
AF:
0.285
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.285
AC:
43139
AN:
151582
Hom.:
6198
Cov.:
33
AF XY:
0.281
AC XY:
20826
AN XY:
74028
show subpopulations
Gnomad4 AFR
AF:
0.275
Gnomad4 AMR
AF:
0.262
Gnomad4 ASJ
AF:
0.337
Gnomad4 EAS
AF:
0.237
Gnomad4 SAS
AF:
0.225
Gnomad4 FIN
AF:
0.276
Gnomad4 NFE
AF:
0.299
Gnomad4 OTH
AF:
0.284
Alfa
AF:
0.284
Hom.:
737
Bravo
AF:
0.281
Asia WGS
AF:
0.230
AC:
794
AN:
3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.67
DANN
Benign
0.61

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1489402; hg19: chr1-79375882; API