1-37976886-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_006802.4(SF3A3):c.1003G>A(p.Gly335Arg) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000378 in 1,585,614 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006802.4 missense, splice_region
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SF3A3 | NM_006802.4 | c.1003G>A | p.Gly335Arg | missense_variant, splice_region_variant | Exon 12 of 17 | ENST00000373019.5 | NP_006793.1 | |
SF3A3 | NM_001320830.2 | c.844G>A | p.Gly282Arg | missense_variant, splice_region_variant | Exon 10 of 15 | NP_001307759.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SF3A3 | ENST00000373019.5 | c.1003G>A | p.Gly335Arg | missense_variant, splice_region_variant | Exon 12 of 17 | 1 | NM_006802.4 | ENSP00000362110.4 | ||
SF3A3 | ENST00000460925.1 | n.548G>A | splice_region_variant, non_coding_transcript_exon_variant | Exon 2 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152140Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000279 AC: 4AN: 1433474Hom.: 0 Cov.: 28 AF XY: 0.00000140 AC XY: 1AN XY: 714980
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1003G>A (p.G335R) alteration is located in exon 12 (coding exon 12) of the SF3A3 gene. This alteration results from a G to A substitution at nucleotide position 1003, causing the glycine (G) at amino acid position 335 to be replaced by an arginine (R). 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