11-66057328-C-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_ModerateBP6_ModerateBS2
The NM_006842.3(SF3B2):āc.730C>Gā(p.Pro244Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000265 in 1,605,730 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 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 -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SF3B2 | NM_006842.3 | c.730C>G | p.Pro244Ala | missense_variant | 7/22 | ENST00000322535.11 | |
SF3B2 | XM_005273726.5 | c.727C>G | p.Pro243Ala | missense_variant | 7/22 | ||
SF3B2 | XM_011544740.4 | c.727C>G | p.Pro243Ala | missense_variant | 7/22 | ||
SF3B2 | XM_017017144.3 | c.724C>G | p.Pro242Ala | missense_variant | 7/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SF3B2 | ENST00000322535.11 | c.730C>G | p.Pro244Ala | missense_variant | 7/22 | 1 | NM_006842.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152190Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000180 AC: 45AN: 249894Hom.: 0 AF XY: 0.000199 AC XY: 27AN XY: 135718
GnomAD4 exome AF: 0.000283 AC: 412AN: 1453540Hom.: 0 Cov.: 29 AF XY: 0.000289 AC XY: 209AN XY: 723664
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152190Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74348
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 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