11-66058911-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006842.3(SF3B2):c.1048C>T(p.Arg350Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,836 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R350Q) has been classified as Likely benign.
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.1048C>T | p.Arg350Trp | missense_variant | 10/22 | ENST00000322535.11 | |
SF3B2 | XM_005273726.5 | c.1045C>T | p.Arg349Trp | missense_variant | 10/22 | ||
SF3B2 | XM_011544740.4 | c.1045C>T | p.Arg349Trp | missense_variant | 10/22 | ||
SF3B2 | XM_017017144.3 | c.1042C>T | p.Arg348Trp | missense_variant | 10/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SF3B2 | ENST00000322535.11 | c.1048C>T | p.Arg350Trp | missense_variant | 10/22 | 1 | NM_006842.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152024Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251292Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135890
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461812Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 727200
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152024Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74226
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 28, 2023 | The c.1048C>T (p.R350W) alteration is located in exon 10 (coding exon 10) of the SF3B2 gene. This alteration results from a C to T substitution at nucleotide position 1048, causing the arginine (R) at amino acid position 350 to be replaced by a tryptophan (W). 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