X-136323266-C-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_153834.4(ADGRG4):c.559C>T(p.Leu187Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000116 in 1,209,357 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 42 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.000027 ( 0 hom., 1 hem., cov: 22)
Exomes 𝑓: 0.00012 ( 0 hom. 41 hem. )
Consequence
ADGRG4
NM_153834.4 missense
NM_153834.4 missense
Scores
1
7
7
Clinical Significance
Conservation
PhyloP100: 0.594
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High Hemizygotes in GnomAdExome4 at 41 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRG4 | NM_153834.4 | c.559C>T | p.Leu187Phe | missense_variant | 5/26 | ENST00000394143.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRG4 | ENST00000394143.6 | c.559C>T | p.Leu187Phe | missense_variant | 5/26 | 1 | NM_153834.4 | P1 | |
ADGRG4 | ENST00000394141.1 | c.70+14419C>T | intron_variant | 1 | |||||
ADGRG4 | ENST00000370652.5 | c.559C>T | p.Leu187Phe | missense_variant | 3/24 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000270 AC: 3AN: 111254Hom.: 0 Cov.: 22 AF XY: 0.0000299 AC XY: 1AN XY: 33428
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GnomAD3 exomes AF: 0.0000873 AC: 16AN: 183185Hom.: 0 AF XY: 0.0000443 AC XY: 3AN XY: 67705
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GnomAD4 exome AF: 0.000125 AC: 137AN: 1098103Hom.: 0 Cov.: 31 AF XY: 0.000113 AC XY: 41AN XY: 363461
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GnomAD4 genome AF: 0.0000270 AC: 3AN: 111254Hom.: 0 Cov.: 22 AF XY: 0.0000299 AC XY: 1AN XY: 33428
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2023 | The c.559C>T (p.L187F) alteration is located in exon 5 (coding exon 2) of the ADGRG4 gene. This alteration results from a C to T substitution at nucleotide position 559, causing the leucine (L) at amino acid position 187 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | May 19, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T
FATHMM_MKL
Benign
D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationTaster
Benign
D;D;N;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Pathogenic
D;D
Polyphen
D;D
Vest4
MVP
MPC
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at