11-66057301-A-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_006842.3(SF3B2):āc.703A>Gā(p.Thr235Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000087 in 1,609,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
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.703A>G | p.Thr235Ala | missense_variant | 7/22 | ENST00000322535.11 | |
SF3B2 | XM_005273726.5 | c.700A>G | p.Thr234Ala | missense_variant | 7/22 | ||
SF3B2 | XM_011544740.4 | c.700A>G | p.Thr234Ala | missense_variant | 7/22 | ||
SF3B2 | XM_017017144.3 | c.697A>G | p.Thr233Ala | missense_variant | 7/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SF3B2 | ENST00000322535.11 | c.703A>G | p.Thr235Ala | missense_variant | 7/22 | 1 | NM_006842.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152052Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000600 AC: 15AN: 250086Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135740
GnomAD4 exome AF: 0.00000686 AC: 10AN: 1457806Hom.: 0 Cov.: 29 AF XY: 0.00000827 AC XY: 6AN XY: 725540
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152170Hom.: 0 Cov.: 31 AF XY: 0.0000538 AC XY: 4AN XY: 74398
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2024 | 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