rs782515760
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001381902.1(SAGE1):c.198C>T(p.Ser66Ser) 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: 23)
Exomes 𝑓: 0.0000027 ( 0 hom. 0 hem. )
Failed GnomAD Quality Control
Consequence
SAGE1
NM_001381902.1 synonymous
NM_001381902.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.203
Publications
1 publications found
Genes affected
SAGE1 (HGNC:30369): (sarcoma antigen 1) This gene belongs to a class of genes that are activated in tumors. These genes are expressed in tumors of different histologic types but not in normal tissues, except for spermatogenic cells and, for some, placenta. The proteins encoded by these genes appear to be strictly tumor specific, and hence may be excellent sources of antigens for cancer immunotherapy. This gene is expressed in sarcomas. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant X-135901669-C-T is Benign according to our data. Variant chrX-135901669-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2661492.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.203 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001381902.1. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
23
GnomAD2 exomes AF: 0.0000112 AC: 2AN: 178601 AF XY: 0.0000158 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
178601
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000274 AC: 3AN: 1093671Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 359211 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
3
AN:
1093671
Hom.:
Cov.:
28
AF XY:
AC XY:
0
AN XY:
359211
show subpopulations
African (AFR)
AF:
AC:
0
AN:
26261
American (AMR)
AF:
AC:
0
AN:
34757
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
19215
East Asian (EAS)
AF:
AC:
0
AN:
30135
South Asian (SAS)
AF:
AC:
0
AN:
53130
European-Finnish (FIN)
AF:
AC:
0
AN:
40421
Middle Eastern (MID)
AF:
AC:
2
AN:
4109
European-Non Finnish (NFE)
AF:
AC:
0
AN:
839730
Other (OTH)
AF:
AC:
1
AN:
45913
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.442
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
23
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (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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