19-2248423-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_007165.5(SF3A2):āc.1272G>Cā(p.Gln424His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000512 in 1,368,350 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_007165.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.1272G>C | p.Gln424His | missense_variant | 9/9 | ENST00000221494.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SF3A2 | ENST00000221494.10 | c.1272G>C | p.Gln424His | missense_variant | 9/9 | 1 | NM_007165.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000665 AC: 1AN: 150460Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.0000286 AC: 1AN: 34948Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 18418
GnomAD4 exome AF: 0.00000493 AC: 6AN: 1217890Hom.: 0 Cov.: 33 AF XY: 0.00000341 AC XY: 2AN XY: 585690
GnomAD4 genome ? AF: 0.00000665 AC: 1AN: 150460Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 73362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 21, 2023 | The c.1272G>C (p.Q424H) alteration is located in exon 9 (coding exon 8) of the SF3A2 gene. This alteration results from a G to C substitution at nucleotide position 1272, causing the glutamine (Q) at amino acid position 424 to be replaced by a histidine (H). 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