rs1057519961
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM5PP2PP3_Moderate
The NM_012433.4(SF3B1):c.1874G>T(p.Arg625Leu) variant causes a missense change involving the alteration of a conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R625C) has been classified as Likely pathogenic.
Frequency
Consequence
NM_012433.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SF3B1 | NM_012433.4 | c.1874G>T | p.Arg625Leu | missense_variant | 14/25 | ENST00000335508.11 | |
SF3B1 | XM_047443838.1 | c.1436G>T | p.Arg479Leu | missense_variant | 11/22 | ||
SF3B1 | XM_047443839.1 | c.1436G>T | p.Arg479Leu | missense_variant | 11/22 | ||
SF3B1 | XM_047443840.1 | c.1874G>T | p.Arg625Leu | missense_variant | 14/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SF3B1 | ENST00000335508.11 | c.1874G>T | p.Arg625Leu | missense_variant | 14/25 | 1 | NM_012433.4 | P1 | |
SF3B1 | ENST00000470268.2 | n.3758G>T | non_coding_transcript_exon_variant | 13/24 | 2 | ||||
SF3B1 | ENST00000652026.1 | c.*2941G>T | 3_prime_UTR_variant, NMD_transcript_variant | 14/25 | |||||
SF3B1 | ENST00000652738.1 | c.*2133G>T | 3_prime_UTR_variant, NMD_transcript_variant | 15/26 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1461746Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 727174
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at