NM_012433.4:c.1998G>T
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 9P and 4B. PP3PP5_Very_StrongBS2
The NM_012433.4(SF3B1):c.1998G>T(p.Lys666Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,613,842 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SF3B1 | NM_012433.4 | c.1998G>T | p.Lys666Asn | missense_variant | Exon 14 of 25 | ENST00000335508.11 | NP_036565.2 | |
SF3B1 | XM_047443838.1 | c.1560G>T | p.Lys520Asn | missense_variant | Exon 11 of 22 | XP_047299794.1 | ||
SF3B1 | XM_047443839.1 | c.1560G>T | p.Lys520Asn | missense_variant | Exon 11 of 22 | XP_047299795.1 | ||
SF3B1 | XM_047443840.1 | c.1998G>T | p.Lys666Asn | missense_variant | Exon 14 of 22 | XP_047299796.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251338Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135830
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461656Hom.: 0 Cov.: 34 AF XY: 0.0000371 AC XY: 27AN XY: 727110
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74342
ClinVar
Submissions by phenotype
Myelodysplastic syndrome Pathogenic:1
- -
Myelodysplastic syndrome progressed to acute myeloid leukemia Pathogenic:1
A mutation that is commonly seen in myelodysplasia with ring sideroblasts. It affects 3'-splice site recognition during pre-mRNA processing. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at