11-66058344-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_006842.3(SF3B2):c.905C>T(p.Ser302Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,613,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006842.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SF3B2 | NM_006842.3 | c.905C>T | p.Ser302Leu | missense_variant | 9/22 | ENST00000322535.11 | |
SF3B2 | XM_005273726.5 | c.902C>T | p.Ser301Leu | missense_variant | 9/22 | ||
SF3B2 | XM_011544740.4 | c.902C>T | p.Ser301Leu | missense_variant | 9/22 | ||
SF3B2 | XM_017017144.3 | c.899C>T | p.Ser300Leu | missense_variant | 9/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SF3B2 | ENST00000322535.11 | c.905C>T | p.Ser302Leu | missense_variant | 9/22 | 1 | NM_006842.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152110Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251392Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135872
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461782Hom.: 0 Cov.: 31 AF XY: 0.0000399 AC XY: 29AN XY: 727192
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152110Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74296
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at