Variant rs3826782 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001974.5(ADGRE1):c.31+86G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0939 in 1,429,386 control chromosomes in the GnomAD database, including 8,009 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 0.090 ( 955 hom., cov: 31)

Exomes 𝑓: 0.094 ( 7054 hom. )

Consequence

ADGRE1
NM_001974.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18

Variant links:

Genes affected

ADGRE1 (HGNC:3336): (adhesion G protein-coupled receptor E1) This gene encodes a protein that has a domain resembling seven transmembrane G protein-coupled hormone receptors (7TM receptors) at its C-terminus. The N-terminus of the encoded protein has six EGF-like modules, separated from the transmembrane segments by a serine/threonine-rich domain, a feature reminiscent of mucin-like, single-span, integral membrane glycoproteins with adhesive properties. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

ADGRE1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADGRE1	NM_001974.5 link	c.31+86G>A		intron_variant		ENST00000312053.9	NP_001965.3	Q14246-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADGRE1	ENST00000312053.9 link	c.31+86G>A		intron_variant		1	NM_001974.5	ENSP00000311545.3		Q14246-1

Frequencies

GnomAD3 genomes

AF:

0.0896

AC:

13633

AN:

152088

Hom.:

958

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0244

Gnomad AMI

AF:

0.189

Gnomad AMR

AF:

0.138

Gnomad ASJ

AF:

0.101

Gnomad EAS

AF:

0.304

Gnomad SAS

AF:

0.0952

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.0881

Gnomad OTH

AF:

0.0990

GnomAD4 exome

AF:

0.0944

AC:

120619

AN:

1277180

Hom.:

7054

AF XY:

0.0943

AC XY:

60348

AN XY:

639816

show subpopulations

Gnomad4 AFR exome

AF:

0.0226

Gnomad4 AMR exome

AF:

0.184

Gnomad4 ASJ exome

AF:

0.114

Gnomad4 EAS exome

AF:

0.282

Gnomad4 SAS exome

AF:

0.0779

Gnomad4 FIN exome

AF:

0.151

Gnomad4 NFE exome

AF:

0.0838

Gnomad4 OTH exome

AF:

0.100

GnomAD4 genome

AF:

0.0896

AC:

13633

AN:

152206

Hom.:

955

Cov.:

AF XY:

0.0954

AC XY:

7096

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.0243

Gnomad4 AMR

AF:

0.138

Gnomad4 ASJ

AF:

0.101

Gnomad4 EAS

AF:

0.304

Gnomad4 SAS

AF:

0.0953

Gnomad4 FIN

AF:

0.163

Gnomad4 NFE

AF:

0.0881

Gnomad4 OTH

AF:

0.0975

Alfa

AF:

0.0932

Hom.:

867

Bravo

AF:

0.0882

Asia WGS

AF:

0.169

AC:

589

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

7.5

DANN

Benign

0.58

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over