chr5-94629103-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_032290.4(SLF1):āc.126T>Cā(p.Asn42=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00728 in 1,541,018 control chromosomes in the GnomAD database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0057 ( 1 hom., cov: 33)
Exomes š: 0.0074 ( 63 hom. )
Consequence
SLF1
NM_032290.4 synonymous
NM_032290.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.304
Genes affected
SLF1 (HGNC:25408): (SMC5-SMC6 complex localization factor 1) Enables ubiquitin protein ligase binding activity. Involved in several processes, including positive regulation of cellular component organization; positive regulation of double-strand break repair; and protein localization to site of double-strand break. Located in nucleoplasm and site of double-strand break. [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=-0.55).
BP6
Variant 5-94629103-T-C is Benign according to our data. Variant chr5-94629103-T-C is described in ClinVar as [Benign]. Clinvar id is 773880.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.304 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 63 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLF1 | NM_032290.4 | c.126T>C | p.Asn42= | synonymous_variant | 3/21 | ENST00000265140.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLF1 | ENST00000265140.10 | c.126T>C | p.Asn42= | synonymous_variant | 3/21 | 2 | NM_032290.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00575 AC: 875AN: 152148Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00680 AC: 1020AN: 149938Hom.: 16 AF XY: 0.00729 AC XY: 576AN XY: 79066
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GnomAD4 exome AF: 0.00744 AC: 10337AN: 1388752Hom.: 63 Cov.: 30 AF XY: 0.00759 AC XY: 5186AN XY: 683686
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GnomAD4 genome AF: 0.00575 AC: 875AN: 152266Hom.: 1 Cov.: 33 AF XY: 0.00548 AC XY: 408AN XY: 74454
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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 | Mar 29, 2018 | - - |
Computational scores
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BayesDel_noAF
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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