19-2248100-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_007165.5(SF3A2):c.949C>A(p.Pro317Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000109 in 1,054,644 control chromosomes in the GnomAD database, including 2 homozygotes. 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_007165.5 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 |
---|---|---|---|---|---|---|---|
SF3A2 | NM_007165.5 | c.949C>A | p.Pro317Thr | missense_variant | 9/9 | ENST00000221494.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SF3A2 | ENST00000221494.10 | c.949C>A | p.Pro317Thr | missense_variant | 9/9 | 1 | NM_007165.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000728 AC: 11AN: 151132Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000513 AC: 7AN: 136386Hom.: 0 AF XY: 0.0000532 AC XY: 4AN XY: 75220
GnomAD4 exome AF: 0.000115 AC: 104AN: 903512Hom.: 2 Cov.: 12 AF XY: 0.000127 AC XY: 59AN XY: 464808
GnomAD4 genome ? AF: 0.0000728 AC: 11AN: 151132Hom.: 0 Cov.: 30 AF XY: 0.0000678 AC XY: 5AN XY: 73768
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 30, 2023 | The c.949C>A (p.P317T) alteration is located in exon 9 (coding exon 8) of the SF3A2 gene. This alteration results from a C to A substitution at nucleotide position 949, causing the proline (P) at amino acid position 317 to be replaced by a threonine (T). 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