rs376668219
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_030962.4(SBF2):c.4699-9C>A variant causes a splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.0000337 in 1,603,090 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
SBF2
NM_030962.4 splice_polypyrimidine_tract, intron
NM_030962.4 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.9583
1
1
Clinical Significance
Conservation
PhyloP100: 4.30
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]
SBF2-AS1 (HGNC:27438): (SBF2 antisense RNA 1)
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.21).
BP6
?
Variant 11-9789351-G-T is Benign according to our data. Variant chr11-9789351-G-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 476933.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SBF2 | NM_030962.4 | c.4699-9C>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000256190.13 | |||
SBF2-AS1 | NR_036485.1 | n.212-18497G>T | intron_variant, non_coding_transcript_variant | ||||
LOC105369149 | XR_007062587.1 | n.356-1518G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SBF2 | ENST00000256190.13 | c.4699-9C>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_030962.4 | P3 | |||
SBF2-AS1 | ENST00000663578.1 | n.237-18497G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000178 AC: 27AN: 152112Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250718Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135730
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GnomAD4 exome AF: 0.0000165 AC: 24AN: 1450860Hom.: 0 Cov.: 28 AF XY: 0.0000194 AC XY: 14AN XY: 722650
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GnomAD4 genome ? AF: 0.000197 AC: 30AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74434
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 01, 2018 | - - |
Charcot-Marie-Tooth disease type 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 10, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at