22-50447066-A-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_002972.4(SBF1):c.*76T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0256 in 1,340,046 control chromosomes in the GnomAD database, including 609 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.017 ( 39 hom., cov: 33)
Exomes 𝑓: 0.027 ( 570 hom. )
Consequence
SBF1
NM_002972.4 3_prime_UTR
NM_002972.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.570
Genes affected
SBF1 (HGNC:10542): (SET binding factor 1) This gene encodes a member of the protein-tyrosine phosphatase family. However, the encoded protein does not appear to be a catalytically active phosphatase because it lacks several amino acids in the catalytic pocket. This protein contains a Guanine nucleotide exchange factor (GEF) domain which is necessary for its role in growth and differentiation. Mutations in this gene have been associated with Charcot-Marie-Tooth disease 4B3. Pseudogenes of this gene have been defined on chromosomes 1 and 8. [provided by RefSeq, Dec 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
?
Variant 22-50447066-A-G is Benign according to our data. Variant chr22-50447066-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1219790.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0166 (2524/152170) while in subpopulation NFE AF= 0.0294 (1996/67962). AF 95% confidence interval is 0.0283. There are 39 homozygotes in gnomad4. There are 1126 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 39 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SBF1 | NM_002972.4 | c.*76T>C | 3_prime_UTR_variant | 41/41 | ENST00000380817.8 | ||
SBF1 | NM_001365819.1 | c.*76T>C | 3_prime_UTR_variant | 40/40 | |||
SBF1 | NM_001410794.1 | c.*76T>C | 3_prime_UTR_variant | 41/41 | |||
SBF1 | NM_001410795.1 | c.*76T>C | 3_prime_UTR_variant | 40/40 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SBF1 | ENST00000380817.8 | c.*76T>C | 3_prime_UTR_variant | 41/41 | 1 | NM_002972.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0166 AC: 2525AN: 152052Hom.: 39 Cov.: 33
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GnomAD4 exome AF: 0.0268 AC: 31830AN: 1187876Hom.: 570 Cov.: 16 AF XY: 0.0261 AC XY: 15475AN XY: 592544
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GnomAD4 genome ? AF: 0.0166 AC: 2524AN: 152170Hom.: 39 Cov.: 33 AF XY: 0.0151 AC XY: 1126AN XY: 74426
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 31, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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