chr12-108523553-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.2796C>T(p.Asn932=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00313 in 1,614,024 control chromosomes in the GnomAD database, including 87 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.014 ( 45 hom., cov: 32)
Exomes 𝑓: 0.0020 ( 42 hom. )
Consequence
SART3
NM_014706.4 synonymous
NM_014706.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.71
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]
FICD (HGNC:18416): (FIC domain protein adenylyltransferase) Enables several functions, including ATP binding activity; Hsp70 protein binding activity; and chaperone binding activity. Involved in protein adenylylation; regulation of IRE1-mediated unfolded protein response; and response to endoplasmic reticulum stress. Is integral component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.69).
BP6
?
Variant 12-108523553-G-A is Benign according to our data. Variant chr12-108523553-G-A is described in ClinVar as [Benign]. Clinvar id is 785423.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.71 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0138 (2101/152246) while in subpopulation AFR AF= 0.0446 (1854/41544). AF 95% confidence interval is 0.0429. There are 45 homozygotes in gnomad4. There are 992 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2098 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SART3 | NM_014706.4 | c.2796C>T | p.Asn932= | synonymous_variant | 19/19 | ENST00000546815.6 | |
SART3 | NM_001410983.1 | c.2850C>T | p.Asn950= | synonymous_variant | 19/19 | ||
SART3 | XM_047429916.1 | c.1932C>T | p.Asn644= | synonymous_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SART3 | ENST00000546815.6 | c.2796C>T | p.Asn932= | synonymous_variant | 19/19 | 5 | NM_014706.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0138 AC: 2098AN: 152128Hom.: 46 Cov.: 32
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GnomAD3 exomes AF: 0.00446 AC: 1120AN: 251298Hom.: 23 AF XY: 0.00350 AC XY: 475AN XY: 135862
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GnomAD4 exome AF: 0.00202 AC: 2949AN: 1461778Hom.: 42 Cov.: 31 AF XY: 0.00192 AC XY: 1398AN XY: 727202
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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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at