17-46923198-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_004287.5(GOSR2):c.6T>C(p.Asp2Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152,088 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Consequence
GOSR2
NM_004287.5 synonymous
NM_004287.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.256
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]
ENSG00000262633 (HGNC:):
LRRC37A2 (HGNC:32404): (leucine rich repeat containing 37 member A2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -11 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
Variant 17-46923198-T-C is Benign according to our data. Variant chr17-46923198-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 700303.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.256 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
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| GOSR2 | NM_004287.5 | MANE Select | c.6T>C | p.Asp2Asp | synonymous | Exon 1 of 6 | NP_004278.2 | ||
| GOSR2 | NM_001321133.2 | c.6T>C | p.Asp2Asp | synonymous | Exon 1 of 7 | NP_001308062.1 | I3NI02 | ||
| GOSR2 | NM_054022.4 | c.6T>C | p.Asp2Asp | synonymous | Exon 1 of 7 | NP_473363.1 | O14653-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| GOSR2 | ENST00000640051.2 | TSL:1 MANE Select | c.6T>C | p.Asp2Asp | synonymous | Exon 1 of 6 | ENSP00000492751.1 | O14653-1 | |
| GOSR2 | ENST00000225567.9 | TSL:1 | c.6T>C | p.Asp2Asp | synonymous | Exon 1 of 7 | ENSP00000225567.4 | O14653-2 | |
| GOSR2 | ENST00000640621.1 | TSL:1 | c.6T>C | p.Asp2Asp | synonymous | Exon 1 of 5 | ENSP00000492830.1 | O14653-3 |
Frequencies
GnomAD3 genomes 0.00000658 AC: 1AN: 152088Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152088
Hom.:
Cov.:
33
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 Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome 0.00000658 AC: 1AN: 152088Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74276 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
152088
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
74276
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41400
American (AMR)
AF:
AC:
0
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5184
South Asian (SAS)
AF:
AC:
0
AN:
4826
European-Finnish (FIN)
AF:
AC:
0
AN:
10600
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
1
AN:
68016
Other (OTH)
AF:
AC:
0
AN:
2088
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Likely benign
Revision:criteria provided, multiple submitters, no conflicts
Pathogenic
VUS
Benign
Condition
-
-
1
Inborn genetic diseases (1)
-
-
1
Progressive myoclonic epilepsy (1)
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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