NM_032787.3:c.1727-3T>A

Variant names:

• chr3-100655896-T-A
• rs9866111
• NM_032787.3:c.1727-3T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_032787.3(ADGRG7):​c.1727-3T>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ADGRG7 NM_032787.3 splice_region, intron
• Scores: Splicing: ADA: 0.09947
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328
• Publications: 14 publications found

Genes affected

ADGRG7 (HGNC:19241): (adhesion G protein-coupled receptor G7) 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 integral component of membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRG7	NM_032787.3	c.1727-3T>A		splice_region_variant, intron_variant	Intron 12 of 15	ENST00000273352.8	NP_116176.2
ADGRG7	NM_001308362.1	c.842-3T>A		splice_region_variant, intron_variant	Intron 6 of 9		NP_001295291.1
ADGRG7	XM_047449088.1	c.1322-3T>A		splice_region_variant, intron_variant	Intron 10 of 13		XP_047305044.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRG7	ENST00000273352.8	c.1727-3T>A		splice_region_variant, intron_variant	Intron 12 of 15	1	NM_032787.3	ENSP00000273352.3
ADGRG7	ENST00000475887.1	c.842-3T>A		splice_region_variant, intron_variant	Intron 6 of 9	2		ENSP00000419788.1
ADGRG7	ENST00000481506.1	n.987-3T>A		splice_region_variant, intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1368712 Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0 AN XY: 685786

African (AFR) AF: 0.00 AC: 0 AN: 32068

American (AMR) AF: 0.00 AC: 0 AN: 44494

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25388

East Asian (EAS) AF: 0.00 AC: 0 AN: 39200

South Asian (SAS) AF: 0.00 AC: 0 AN: 83404

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53148

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5598

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1028308

Other (OTH) AF: 0.00 AC: 0 AN: 57104

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 73475

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	6.5
DANN	Benign	0.69
PhyloP100		-0.33

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.099
dbscSNV1_RF	Benign	0.33
SpliceAI score (max)		0.35		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.35		Position offset: 3

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

Other links and lift over

dbSNP: rs9866111; hg19: chr3-100374740;