rs139896661
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_015559.3(SETBP1):c.4290G>A(p.Val1430=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000391 in 1,613,838 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. V1430V) has been classified as Likely benign.
Frequency
Consequence
NM_015559.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SETBP1 | NM_015559.3 | c.4290G>A | p.Val1430= | synonymous_variant | 6/6 | ENST00000649279.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SETBP1 | ENST00000649279.2 | c.4290G>A | p.Val1430= | synonymous_variant | 6/6 | NM_015559.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000441 AC: 67AN: 151960Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000593 AC: 149AN: 251306Hom.: 0 AF XY: 0.000589 AC XY: 80AN XY: 135890
GnomAD4 exome AF: 0.000386 AC: 564AN: 1461878Hom.: 0 Cov.: 33 AF XY: 0.000364 AC XY: 265AN XY: 727238
GnomAD4 genome ? AF: 0.000441 AC: 67AN: 151960Hom.: 1 Cov.: 32 AF XY: 0.000620 AC XY: 46AN XY: 74210
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 15, 2014 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 07, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at