19-2247888-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_007165.5(SF3A2):c.737C>T(p.Pro246Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000444 in 1,578,046 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 Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SF3A2 | NM_007165.5 | c.737C>T | p.Pro246Leu | missense_variant | 9/9 | ENST00000221494.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SF3A2 | ENST00000221494.10 | c.737C>T | p.Pro246Leu | missense_variant | 9/9 | 1 | NM_007165.5 | P1 | |
SF3A2 | ENST00000592314.5 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000660 AC: 1AN: 151544Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000886 AC: 2AN: 225708Hom.: 0 AF XY: 0.0000159 AC XY: 2AN XY: 125872
GnomAD4 exome AF: 0.00000421 AC: 6AN: 1426502Hom.: 0 Cov.: 29 AF XY: 0.00000281 AC XY: 2AN XY: 711430
GnomAD4 genome ? AF: 0.00000660 AC: 1AN: 151544Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74002
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.737C>T (p.P246L) 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 737, causing the proline (P) at amino acid position 246 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