19-6927985-A-G

Variant names:

• chr19-6927985-A-G
• rs3895916
• NM_001974.5:c.2223-160A>G

Variant summary

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

The NM_001974.5(ADGRE1):​c.2223-160A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,972 control chromosomes in the GnomAD database, including 25,199 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 0.54 (25199 hom., cov: 31)
• Consequence: ADGRE1 NM_001974.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615
• Publications: 5 publications found

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]

LOC105372256 (HGNC:):

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 = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRE1	NM_001974.5	c.2223-160A>G		intron_variant	Intron 16 of 20	ENST00000312053.9	NP_001965.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRE1	ENST00000312053.9	c.2223-160A>G		intron_variant	Intron 16 of 20	1	NM_001974.5	ENSP00000311545.3

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82628 AN: 151854 Hom.: 25141 Cov.: 31

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.545 AC: 82749 AN: 151972 Hom.: 25199 Cov.: 31 AF XY: 0.536 AC XY: 39835 AN XY: 74256

African (AFR) AF: 0.824 AC: 34153 AN: 41464

American (AMR) AF: 0.479 AC: 7311 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1822 AN: 3468

East Asian (EAS) AF: 0.184 AC: 951 AN: 5170

South Asian (SAS) AF: 0.398 AC: 1916 AN: 4810

European-Finnish (FIN) AF: 0.386 AC: 4071 AN: 10536

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30979 AN: 67950

Other (OTH) AF: 0.545 AC: 1151 AN: 2112

Alfa AF: 0.506 Hom.: 37704

Bravo AF: 0.561

Asia WGS AF: 0.438 AC: 1524 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	0.80
DANN	Benign	0.27
PhyloP100		-0.61
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3895916; hg19: chr19-6927996;