chr11-66058930-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006842.3(SF3B2):c.1067G>A(p.Arg356Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,614,028 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006842.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SF3B2 | NM_006842.3 | c.1067G>A | p.Arg356Gln | missense_variant | 10/22 | ENST00000322535.11 | |
SF3B2 | XM_005273726.5 | c.1064G>A | p.Arg355Gln | missense_variant | 10/22 | ||
SF3B2 | XM_011544740.4 | c.1064G>A | p.Arg355Gln | missense_variant | 10/22 | ||
SF3B2 | XM_017017144.3 | c.1061G>A | p.Arg354Gln | missense_variant | 10/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SF3B2 | ENST00000322535.11 | c.1067G>A | p.Arg356Gln | missense_variant | 10/22 | 1 | NM_006842.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152160Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461868Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727236
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152160Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74346
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.1067G>A (p.R356Q) alteration is located in exon 10 (coding exon 10) of the SF3B2 gene. This alteration results from a G to A substitution at nucleotide position 1067, causing the arginine (R) at amino acid position 356 to be replaced by a glutamine (Q). 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