NM_001974.5:c.31+86G>A

Variant names:

• chr19-6887725-G-A
• rs3826782
• NM_001974.5:c.31+86G>A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 6 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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ADGRE1	NM_001974.5	c.31+86G>A		intron_variant	Intron 1 of 20	ENST00000312053.9	NP_001965.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRE1	ENST00000312053.9	c.31+86G>A		intron_variant	Intron 1 of 20	1	NM_001974.5	ENSP00000311545.3

Frequencies

GnomAD3 genomes AF: 0.0896 AC: 13633 AN: 152088 Hom.: 958 Cov.: 31

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

African (AFR) AF: 0.0226 AC: 617 AN: 27324

American (AMR) AF: 0.184 AC: 5542 AN: 30140

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 2586 AN: 22632

East Asian (EAS) AF: 0.282 AC: 10383 AN: 36792

South Asian (SAS) AF: 0.0779 AC: 5790 AN: 74280

European-Finnish (FIN) AF: 0.151 AC: 7935 AN: 52392

Middle Eastern (MID) AF: 0.133 AC: 634 AN: 4772

European-Non Finnish (NFE) AF: 0.0838 AC: 81761 AN: 975154

Other (OTH) AF: 0.100 AC: 5371 AN: 53694

GnomAD4 genome AF: 0.0896 AC: 13633 AN: 152206 Hom.: 955 Cov.: 31 AF XY: 0.0954 AC XY: 7096 AN XY: 74410

African (AFR) AF: 0.0243 AC: 1009 AN: 41550

American (AMR) AF: 0.138 AC: 2116 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3470

East Asian (EAS) AF: 0.304 AC: 1571 AN: 5168

South Asian (SAS) AF: 0.0953 AC: 459 AN: 4818

European-Finnish (FIN) AF: 0.163 AC: 1725 AN: 10596

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0881 AC: 5989 AN: 68004

Other (OTH) AF: 0.0975 AC: 206 AN: 2112

Alfa AF: 0.0882 Hom.: 1227

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
PhyloP100		1.2
PromoterAI		-0.0050	Neutral
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: rs3826782; hg19: chr19-6887736; COSMIC: COSV51672964; COSMIC: COSV51672964;