rs79251068
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_030962.4(SBF2):āc.4533A>Gā(p.Thr1511=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00172 in 1,613,820 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.0097 ( 20 hom., cov: 32)
Exomes š: 0.00089 ( 24 hom. )
Consequence
SBF2
NM_030962.4 synonymous
NM_030962.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.74
Genes affected
SBF2 (HGNC:2135): (SET binding factor 2) This gene encodes a pseudophosphatase and member of the myotubularin-related protein family. This gene maps within the CMT4B2 candidate region of chromosome 11p15 and mutations in this gene have been associated with Charcot-Marie-Tooth Disease, type 4B2. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
?
Variant 11-9795868-T-C is Benign according to our data. Variant chr11-9795868-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 306582.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-9795868-T-C is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=1.74 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00975 (1484/152270) while in subpopulation AFR AF= 0.034 (1412/41544). AF 95% confidence interval is 0.0325. There are 20 homozygotes in gnomad4. There are 709 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 20 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SBF2 | NM_030962.4 | c.4533A>G | p.Thr1511= | synonymous_variant | 33/40 | ENST00000256190.13 | |
SBF2-AS1 | NR_036485.1 | n.212-11980T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SBF2 | ENST00000256190.13 | c.4533A>G | p.Thr1511= | synonymous_variant | 33/40 | 1 | NM_030962.4 | P3 | |
SBF2-AS1 | ENST00000663578.1 | n.237-11980T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00976 AC: 1485AN: 152152Hom.: 20 Cov.: 32
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GnomAD3 exomes AF: 0.00260 AC: 654AN: 251216Hom.: 11 AF XY: 0.00175 AC XY: 238AN XY: 135802
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GnomAD4 exome AF: 0.000888 AC: 1298AN: 1461550Hom.: 24 Cov.: 31 AF XY: 0.000809 AC XY: 588AN XY: 727084
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GnomAD4 genome ? AF: 0.00975 AC: 1484AN: 152270Hom.: 20 Cov.: 32 AF XY: 0.00952 AC XY: 709AN XY: 74456
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 22, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Charcot-Marie-Tooth disease Benign:1
Benign, criteria provided, single submitter | clinical testing | Molecular Genetics Laboratory, London Health Sciences Centre | - | - - |
Charcot-Marie-Tooth disease type 4B2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 08, 2018 | - - |
Charcot-Marie-Tooth disease type 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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