19-2248299-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007165.5(SF3A2):c.1148C>A(p.Ala383Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000016 in 1,251,156 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SF3A2 | NM_007165.5 | c.1148C>A | p.Ala383Asp | missense_variant | 9/9 | ENST00000221494.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SF3A2 | ENST00000221494.10 | c.1148C>A | p.Ala383Asp | missense_variant | 9/9 | 1 | NM_007165.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 27
GnomAD3 exomes AF: 0.0000281 AC: 1AN: 35636Hom.: 0 AF XY: 0.0000528 AC XY: 1AN XY: 18926
GnomAD4 exome AF: 0.00000160 AC: 2AN: 1251156Hom.: 0 Cov.: 33 AF XY: 0.00000330 AC XY: 2AN XY: 605520
GnomAD4 genome ? Cov.: 27
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 30, 2023 | The c.1148C>A (p.A383D) 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 1148, causing the alanine (A) at amino acid position 383 to be replaced by an aspartic acid (D). 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