5-90724971-G-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP6_ModerateBP7
The NM_032119.4(ADGRV1):c.9888G>T(p.Gly3296Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000276 in 1,448,770 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. G3296G) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000028 ( 0 hom. )
Consequence
ADGRV1
NM_032119.4 synonymous
NM_032119.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0560
Publications
0 publications found
Genes affected
ADGRV1 (HGNC:17416): (adhesion G protein-coupled receptor V1) This gene encodes a member of the G-protein coupled receptor superfamily. The encoded protein contains a 7-transmembrane receptor domain, binds calcium and is expressed in the central nervous system. Mutations in this gene are associated with Usher syndrome 2 and familial febrile seizures. Several alternatively spliced transcripts have been described. [provided by RefSeq, Jul 2008]
ADGRV1 Gene-Disease associations (from GenCC):
- Usher syndrome type 2Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
- Usher syndrome type 2CInheritance: AR Classification: STRONG Submitted by: G2P, PanelApp Australia, Labcorp Genetics (formerly Invitae)
- febrile seizures, familial, 4Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
- nonsyndromic genetic hearing lossInheritance: AR Classification: NO_KNOWN Submitted by: ClinGen
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 5-90724971-G-T is Benign according to our data. Variant chr5-90724971-G-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2967388.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.056 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ADGRV1 | NM_032119.4 | c.9888G>T | p.Gly3296Gly | synonymous_variant | Exon 46 of 90 | ENST00000405460.9 | NP_115495.3 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ADGRV1 | ENST00000405460.9 | c.9888G>T | p.Gly3296Gly | synonymous_variant | Exon 46 of 90 | 1 | NM_032119.4 | ENSP00000384582.2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000276 AC: 4AN: 1448770Hom.: 0 Cov.: 29 AF XY: 0.00000278 AC XY: 2AN XY: 720118 show subpopulations
GnomAD4 exome
AF:
AC:
4
AN:
1448770
Hom.:
Cov.:
29
AF XY:
AC XY:
2
AN XY:
720118
show subpopulations
African (AFR)
AF:
AC:
0
AN:
32672
American (AMR)
AF:
AC:
0
AN:
42130
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25936
East Asian (EAS)
AF:
AC:
0
AN:
39420
South Asian (SAS)
AF:
AC:
0
AN:
82124
European-Finnish (FIN)
AF:
AC:
0
AN:
53320
Middle Eastern (MID)
AF:
AC:
0
AN:
5742
European-Non Finnish (NFE)
AF:
AC:
4
AN:
1107542
Other (OTH)
AF:
AC:
0
AN:
59884
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.488
Heterozygous variant carriers
0
1
1
2
2
3
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0.20
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0.60
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
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8
10
<30
30-35
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40-45
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Aug 18, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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