16-70541800-A-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_012426.5(SF3B3):c.1199A>T(p.Glu400Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000752 in 1,461,804 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 Uncertain significance (★).
Frequency
Consequence
NM_012426.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SF3B3 | ENST00000302516.10 | c.1199A>T | p.Glu400Val | missense_variant | Exon 9 of 26 | 1 | NM_012426.5 | ENSP00000305790.5 | ||
SF3B3 | ENST00000567635.5 | n.62A>T | non_coding_transcript_exon_variant | Exon 1 of 7 | 5 | ENSP00000463253.1 | ||||
SF3B3 | ENST00000572365.1 | n.302A>T | non_coding_transcript_exon_variant | Exon 3 of 5 | 4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251376Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135854
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461804Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727202
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1199A>T (p.E400V) alteration is located in exon 9 (coding exon 8) of the SF3B3 gene. This alteration results from a A to T substitution at nucleotide position 1199, causing the glutamic acid (E) at amino acid position 400 to be replaced by a valine (V). 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