rs803191

Positions:

• chrX-136380607-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_153834.4(ADGRG4):​c.7777-7133T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.019 (3 hom., 12 hem., cov: 0)
• Consequence: ADGRG4 NM_153834.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

ADGRG4 (HGNC:18992): (adhesion G protein-coupled receptor G4) This gene encodes a G-protein coupled receptor belonging to a large family of diverse integral membrane proteins that participate in various physiological functions. Members of this superfamily are characterized by a signature 7-transmembrane domain motif. The ligand for this family member is unknown, and it is therefore an orphan receptor. This receptor is known to be expressed in normal enterochromaffin cells and in gastrointestinal neuroendocrine carcinoma cells, and it is therefore considered to be a novel biomarker or target for immunotherapy. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0191 (577/30205) while in subpopulation AFR AF= 0.0339 (282/8316). AF 95% confidence interval is 0.0307. There are 3 homozygotes in gnomad4. There are 12 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADGRG4	NM_153834.4	c.7777-7133T>C		intron_variant		ENST00000394143.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADGRG4	ENST00000394143.6	c.7777-7133T>C		intron_variant		1	NM_153834.4	P1
ADGRG4	ENST00000394141.1	c.7162-7133T>C		intron_variant		1
ADGRG4	ENST00000370652.5	c.7777-7133T>C		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.0191 AC: 577 AN: 30191 Hom.: 3 Cov.: 0 AF XY: 0.00178 AC XY: 12 AN XY: 6729

Gnomad AFR AF: 0.0340

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0120

Gnomad ASJ AF: 0.00119

Gnomad EAS AF: 0.0325

Gnomad SAS AF: 0.00607

Gnomad FIN AF: 0.00801

Gnomad MID AF: 0.0143

Gnomad NFE AF: 0.0143

Gnomad OTH AF: 0.0167

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

GnomAD4 genome AF: 0.0191 AC: 577 AN: 30205 Hom.: 3 Cov.: 0 AF XY: 0.00178 AC XY: 12 AN XY: 6741

Gnomad4 AFR AF: 0.0339

Gnomad4 AMR AF: 0.0120

Gnomad4 ASJ AF: 0.00119

Gnomad4 EAS AF: 0.0327

Gnomad4 SAS AF: 0.00607

Gnomad4 FIN AF: 0.00801

Gnomad4 NFE AF: 0.0143

Gnomad4 OTH AF: 0.0164

Alfa AF: 0.0793 Hom.: 65

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.2
DANN	Benign	0.17

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

Other links and lift over

dbSNP: rs803191; hg19: chrX-135462766;