19-2248401-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_007165.5(SF3A2):c.1250C>T(p.Ser417Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000159 in 1,381,130 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_007165.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SF3A2 | NM_007165.5 | c.1250C>T | p.Ser417Leu | missense_variant | 9/9 | ENST00000221494.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SF3A2 | ENST00000221494.10 | c.1250C>T | p.Ser417Leu | missense_variant | 9/9 | 1 | NM_007165.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000528 AC: 8AN: 151458Hom.: 0 Cov.: 28
GnomAD4 exome AF: 0.0000114 AC: 14AN: 1229554Hom.: 0 Cov.: 34 AF XY: 0.0000101 AC XY: 6AN XY: 592202
GnomAD4 genome AF: 0.0000528 AC: 8AN: 151576Hom.: 0 Cov.: 28 AF XY: 0.000108 AC XY: 8AN XY: 74074
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 13, 2023 | The c.1250C>T (p.S417L) alteration is located in exon 9 (coding exon 8) of the SF3A2 gene. This alteration results from a C to T substitution at nucleotide position 1250, causing the serine (S) at amino acid position 417 to be replaced by a leucine (L). 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