17-46931103-A-G
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_004287.5(GOSR2):c.99A>G(p.Val33Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
GOSR2
NM_004287.5 synonymous
NM_004287.5 synonymous
Scores
1
3
Clinical Significance
Conservation
PhyloP100: 1.78
Publications
0 publications found
Genes affected
GOSR2 (HGNC:4431): (golgi SNAP receptor complex member 2) This gene encodes a trafficking membrane protein which transports proteins among the medial- and trans-Golgi compartments. Due to its chromosomal location and trafficking function, this gene may be involved in familial essential hypertension. [provided by RefSeq, Mar 2016]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 17-46931103-A-G is Benign according to our data. Variant chr17-46931103-A-G is described in ClinVar as Likely_benign. ClinVar VariationId is 462918.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.78 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_004287.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| GOSR2 | NM_004287.5 | MANE Select | c.99A>G | p.Val33Val | synonymous | Exon 3 of 6 | NP_004278.2 | ||
| GOSR2 | NM_001353114.2 | c.96A>G | p.Ile32Met | missense splice_region | Exon 3 of 6 | NP_001340043.1 | |||
| GOSR2 | NM_001353116.2 | c.96A>G | p.Ile32Met | missense splice_region | Exon 3 of 6 | NP_001340045.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| GOSR2 | ENST00000640051.2 | TSL:1 MANE Select | c.99A>G | p.Val33Val | synonymous | Exon 3 of 6 | ENSP00000492751.1 | ||
| GOSR2 | ENST00000225567.9 | TSL:1 | c.99A>G | p.Val33Val | synonymous | Exon 3 of 7 | ENSP00000225567.4 | ||
| GOSR2 | ENST00000640621.1 | TSL:1 | c.99A>G | p.Val33Val | synonymous | Exon 3 of 5 | ENSP00000492830.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1404802Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 702640
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1404802
Hom.:
Cov.:
25
AF XY:
AC XY:
0
AN XY:
702640
African (AFR)
AF:
AC:
0
AN:
32396
American (AMR)
AF:
AC:
0
AN:
44654
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25806
East Asian (EAS)
AF:
AC:
0
AN:
39406
South Asian (SAS)
AF:
AC:
0
AN:
85046
European-Finnish (FIN)
AF:
AC:
0
AN:
53382
Middle Eastern (MID)
AF:
AC:
0
AN:
5226
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1060486
Other (OTH)
AF:
AC:
0
AN:
58400
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Progressive myoclonic epilepsy Benign:1
Apr 20, 2017
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
AlphaMissense
Benign
BayesDel_noAF
Benign
DANN
Benign
FATHMM_MKL
Uncertain
D
PhyloP100
GERP RS
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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