chr12-108526396-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_014706.4(SART3):c.2073C>T(p.Asp691=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00421 in 1,614,098 control chromosomes in the GnomAD database, including 52 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0037 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0043 ( 51 hom. )
Consequence
SART3
NM_014706.4 synonymous
NM_014706.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0850
Genes affected
SART3 (HGNC:16860): (spliceosome associated factor 3, U4/U6 recycling protein) The protein encoded by this gene is an RNA-binding nuclear protein that is a tumor-rejection antigen. This antigen possesses tumor epitopes capable of inducing HLA-A24-restricted and tumor-specific cytotoxic T lymphocytes in cancer patients and may be useful for specific immunotherapy. This gene product is found to be an important cellular factor for HIV-1 gene expression and viral replication. It also associates transiently with U6 and U4/U6 snRNPs during the recycling phase of the spliceosome cycle. This encoded protein is thought to be involved in the regulation of mRNA splicing. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
?
Variant 12-108526396-G-A is Benign according to our data. Variant chr12-108526396-G-A is described in ClinVar as [Benign]. Clinvar id is 788887.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.085 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00427 (6243/1461776) while in subpopulation MID AF= 0.0194 (112/5768). AF 95% confidence interval is 0.0165. There are 51 homozygotes in gnomad4_exome. There are 3504 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 561 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SART3 | NM_014706.4 | c.2073C>T | p.Asp691= | synonymous_variant | 16/19 | ENST00000546815.6 | |
SART3 | NM_001410983.1 | c.2127C>T | p.Asp709= | synonymous_variant | 16/19 | ||
SART3 | XM_047429916.1 | c.1209C>T | p.Asp403= | synonymous_variant | 11/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SART3 | ENST00000546815.6 | c.2073C>T | p.Asp691= | synonymous_variant | 16/19 | 5 | NM_014706.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00369 AC: 561AN: 152204Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.00572 AC: 1439AN: 251424Hom.: 17 AF XY: 0.00657 AC XY: 893AN XY: 135890
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GnomAD4 exome AF: 0.00427 AC: 6243AN: 1461776Hom.: 51 Cov.: 32 AF XY: 0.00482 AC XY: 3504AN XY: 727176
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at