X-136344382-A-AT
Position:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_153834.4(ADGRG4):c.686-3dup variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000719 in 1,112,341 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000027 ( 0 hom., 1 hem., cov: 23)
Exomes 𝑓: 0.0000050 ( 0 hom. 2 hem. )
Consequence
ADGRG4
NM_153834.4 splice_polypyrimidine_tract, intron
NM_153834.4 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.230
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
Variant X-136344382-A-AT is Benign according to our data. Variant chrX-136344382-A-AT is described in ClinVar as [Likely_benign]. Clinvar id is 3050739.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Hemizygotes in GnomAdExome4 at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRG4 | NM_153834.4 | c.686-3dup | splice_polypyrimidine_tract_variant, intron_variant | ENST00000394143.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRG4 | ENST00000394143.6 | c.686-3dup | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_153834.4 | P1 | |||
ADGRG4 | ENST00000394141.1 | c.71-3dup | splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
ADGRG4 | ENST00000370652.5 | c.686-3dup | splice_polypyrimidine_tract_variant, intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000268 AC: 3AN: 112096Hom.: 0 Cov.: 23 AF XY: 0.0000292 AC XY: 1AN XY: 34302
GnomAD3 genomes
AF:
AC:
3
AN:
112096
Hom.:
Cov.:
23
AF XY:
AC XY:
1
AN XY:
34302
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000500 AC: 5AN: 1000197Hom.: 0 Cov.: 20 AF XY: 0.00000662 AC XY: 2AN XY: 302045
GnomAD4 exome
AF:
AC:
5
AN:
1000197
Hom.:
Cov.:
20
AF XY:
AC XY:
2
AN XY:
302045
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000268 AC: 3AN: 112144Hom.: 0 Cov.: 23 AF XY: 0.0000291 AC XY: 1AN XY: 34360
GnomAD4 genome
AF:
AC:
3
AN:
112144
Hom.:
Cov.:
23
AF XY:
AC XY:
1
AN XY:
34360
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
ADGRG4-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 01, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at