22-30342208-T-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_005877.6(SF3A1):c.869A>G(p.Asn290Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000874 in 1,614,062 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005877.6 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 |
---|---|---|---|---|---|---|---|
SF3A1 | NM_005877.6 | c.869A>G | p.Asn290Ser | missense_variant | 6/16 | ENST00000215793.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SF3A1 | ENST00000215793.13 | c.869A>G | p.Asn290Ser | missense_variant | 6/16 | 1 | NM_005877.6 | P1 | |
SF3A1 | ENST00000411423.1 | c.64-3029A>G | intron_variant, NMD_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000925 AC: 23AN: 248602Hom.: 0 AF XY: 0.0000892 AC XY: 12AN XY: 134600
GnomAD4 exome AF: 0.0000835 AC: 122AN: 1461880Hom.: 0 Cov.: 34 AF XY: 0.0000784 AC XY: 57AN XY: 727244
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 19, 2023 | The c.869A>G (p.N290S) alteration is located in exon 6 (coding exon 6) of the SF3A1 gene. This alteration results from a A to G substitution at nucleotide position 869, causing the asparagine (N) at amino acid position 290 to be replaced by a serine (S). 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