rs374250186
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PM5PP3_Moderate
The NM_012433.4(SF3B1):c.1997A>T(p.Lys666Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,958 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. K666E) has been classified as Likely pathogenic.
Frequency
Consequence
NM_012433.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SF3B1 | NM_012433.4 | c.1997A>T | p.Lys666Met | missense_variant | 14/25 | ENST00000335508.11 | |
SF3B1 | XM_047443838.1 | c.1559A>T | p.Lys520Met | missense_variant | 11/22 | ||
SF3B1 | XM_047443839.1 | c.1559A>T | p.Lys520Met | missense_variant | 11/22 | ||
SF3B1 | XM_047443840.1 | c.1997A>T | p.Lys666Met | missense_variant | 14/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SF3B1 | ENST00000335508.11 | c.1997A>T | p.Lys666Met | missense_variant | 14/25 | 1 | NM_012433.4 | P1 | |
SF3B1 | ENST00000470268.2 | n.3881A>T | non_coding_transcript_exon_variant | 13/24 | 2 | ||||
SF3B1 | ENST00000652026.1 | c.*3064A>T | 3_prime_UTR_variant, NMD_transcript_variant | 14/25 | |||||
SF3B1 | ENST00000652738.1 | c.*2256A>T | 3_prime_UTR_variant, NMD_transcript_variant | 15/26 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152222Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461736Hom.: 0 Cov.: 34 AF XY: 0.00000413 AC XY: 3AN XY: 727176
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74382
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at