rs9866111
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_032787.3(ADGRG7):c.1727-3T>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 2/2 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, splice_polypyrimidine_tract, intron
NM_032787.3 splice_region, splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.09947
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.328
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRG7 | NM_032787.3 | c.1727-3T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000273352.8 | |||
ADGRG7 | NM_001308362.1 | c.842-3T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
ADGRG7 | XM_047449088.1 | c.1322-3T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRG7 | ENST00000273352.8 | c.1727-3T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_032787.3 | P1 | |||
ADGRG7 | ENST00000475887.1 | c.842-3T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
ADGRG7 | ENST00000481506.1 | n.987-3T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1368712Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0AN XY: 685786
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1368712
Hom.:
Cov.:
20
AF XY:
AC XY:
0
AN XY:
685786
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: 3
Find out detailed SpliceAI scores and Pangolin per-transcript scores at