16-70561649-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP2PP3
The NM_012426.5(SF3B3):c.2153G>A(p.Arg718His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012426.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SF3B3 | NM_012426.5 | c.2153G>A | p.Arg718His | missense_variant | 17/26 | ENST00000302516.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SF3B3 | ENST00000302516.10 | c.2153G>A | p.Arg718His | missense_variant | 17/26 | 1 | NM_012426.5 | P1 | |
SF3B3 | ENST00000563739.5 | n.301G>A | non_coding_transcript_exon_variant | 1/5 | 2 | ||||
SF3B3 | ENST00000568539.1 | n.262G>A | non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1461616Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727134
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 03, 2022 | The c.2153G>A (p.R718H) alteration is located in exon 17 (coding exon 16) of the SF3B3 gene. This alteration results from a G to A substitution at nucleotide position 2153, causing the arginine (R) at amino acid position 718 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.