chr1-35190780-T-C
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_005066.3(SFPQ):āc.1233A>Gā(p.Thr411=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00288 in 1,614,242 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0029 ( 4 hom., cov: 33)
Exomes š: 0.0029 ( 6 hom. )
Consequence
SFPQ
NM_005066.3 synonymous
NM_005066.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.343
Genes affected
SFPQ (HGNC:10774): (splicing factor proline and glutamine rich) Enables DNA binding activity; histone deacetylase binding activity; and protein homodimerization activity. Involved in several processes, including alternative mRNA splicing, via spliceosome; positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway; and regulation of transcription by RNA polymerase II. Acts upstream of or within double-strand break repair via homologous recombination. Located in chromatin; nuclear matrix; and paraspeckles. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant 1-35190780-T-C is Benign according to our data. Variant chr1-35190780-T-C is described in ClinVar as [Benign]. Clinvar id is 712023.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.343 with no splicing effect.
BS2
High AC in GnomAd4 at 436 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SFPQ | NM_005066.3 | c.1233A>G | p.Thr411= | synonymous_variant | 3/10 | ENST00000357214.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFPQ | ENST00000357214.6 | c.1233A>G | p.Thr411= | synonymous_variant | 3/10 | 1 | NM_005066.3 | P1 | |
SFPQ | ENST00000696553.1 | c.1296A>G | p.Thr432= | synonymous_variant | 3/10 |
Frequencies
GnomAD3 genomes AF: 0.00286 AC: 436AN: 152236Hom.: 4 Cov.: 33
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GnomAD3 exomes AF: 0.00286 AC: 718AN: 251416Hom.: 0 AF XY: 0.00271 AC XY: 368AN XY: 135872
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GnomAD4 exome AF: 0.00288 AC: 4211AN: 1461888Hom.: 6 Cov.: 32 AF XY: 0.00282 AC XY: 2049AN XY: 727244
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GnomAD4 genome AF: 0.00286 AC: 436AN: 152354Hom.: 4 Cov.: 33 AF XY: 0.00295 AC XY: 220AN XY: 74492
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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 | Sep 05, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at